NIF-Investigation
type: Ontology
imports: BIRNLex-OBI-proxy.ttl
imports: cogat v0.3.owl
imports: CogPO.ttl
imports: NIF-Government-Granting-Agency.ttl
imports: NIF-Resource.ttl
imports: NIF-Scientific-Discipline.ttl
imports: nif backend.ttl
change note: v.1.2 (July, 2009) - New classes have been added from NeuroLex wiki since the February release (Class ID: nlx_inv_20090401 to 20090610). v 2.0 (August, 2011) - NIF-Investigation now imports NIF-Resource.owl, NIF-Government-Granting-Agency.owl, and NIF-Scientific-discipline.owl as part of its direct imports. Imports Cognitive paradigm ontology (CogPO). v 2.1 (April, 2012) - Modified the hierarchy of 'Data set'. all the subclasses of 'Data set' are kept as 'Information content entity'. The reason for this chage was to provide a cleaner hierarchy for NIF Resource descriptor. v2.2 (October, 2012) - New classes added under Electron microscopic imaging assay. Definition changed for Segmentation Software from NITRC. v2.3 (December, 2012) - Addition of NEMO (v.2.98) as an imported module. Addition of Cognitive Atlas Ontology (CogAt v.0.3) as an import. Note that we have only imported the 'concepts' and excluded the 'task' classes for now. Newly defined classes: Neuroimaging and Immunolabeling.
version info: 2.3; December 1, 2012

R-weighted back projection
type: Class
subclass of: Image reconstruction algorithm
editorial note: Adapted from IMOD user manual. Kremer JR, Mastronarde DN, McIntosh JR. Computer visualization of three-dimensional image data using IMOD. J Struct Biol. 1996 Jan-Feb;116(1):71-6.
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A reconstruction algorithm for electron tomography. In R-weighted backprojection, each horizontal line of input data is filtered to weight each spatial frequency proportional to its radius in Fourier space. This is radial weighting, and the filter is referred to as a radial filter.
bonfire ID: BF_T0000139
has birnlex curator: Maryann Martone
has curation status: uncurated

Normal control group
type: Class
deprecated: true
subclass of: DeprecatedClass
created date: 2006-06-01
modified date: 2007-03-05
birnlex definition: A subject group consisting of individuals that display a canonical phenotype for the phenotype under investigation in a scientific study. Membership in this group does not imply that the subject displays no abberrant phenotypes. For example, an adult that displays no symptoms of respiratory disease may serve as a normal control in a study even though the subject posssess a rare blood type.
bonfire ID: BF_T0000217
has former parent class: birnlexInvestigation 174

Structural MRI platform
type: Class
synonym: MRI platform
subclass of: Magnetic resonance imaging platform
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Action observation paradigm
type: Class
synonym: Action Observation
subclass of: Behavioral paradigm
disjoint with: Episodic recall paradigm
disjoint with: Breathhold paradigm
disjoint with: Acupuncture paradigm
disjoint with: Divided auditory attention paradigm
disjoint with: Encoding paradigm
disjoint with: Classical conditioning paradigm
disjoint with: Serial item recognition paradigm
disjoint with: Sensorimotor paradigm
disjoint with: Delayed matching to sample paradigm
disjoint with: Drawing paradigm
disjoint with: Oddball discrimination paradigm
disjoint with: Mismatch negativity paradigm
disjoint with: Deductive reasoning paradigm
disjoint with: Eye Saccade paradigm
disjoint with: Reading paradigm
disjoint with: Eating paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A behavioral paradigm in which subjects view images of moving body parts (Brain Map).
bonfire ID: BF_T0000338
has birnlex curator: Jessica Turner
has curation status: pending final vetting
has external source: BrainMap.org
pending action note: Clarify the exact nature of this task

Sample sectioning
type: Class
subclass of: Specimen preparation
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Episodic recall paradigm
type: Class
subclass of: Behavioral paradigm
disjoint with: Breathhold paradigm
disjoint with: Acupuncture paradigm
disjoint with: Divided auditory attention paradigm
disjoint with: Encoding paradigm
disjoint with: Classical conditioning paradigm
disjoint with: Serial item recognition paradigm
disjoint with: Sensorimotor paradigm
disjoint with: Delayed matching to sample paradigm
disjoint with: Drawing paradigm
disjoint with: Oddball discrimination paradigm
disjoint with: Mismatch negativity paradigm
disjoint with: Deductive reasoning paradigm
disjoint with: Eye Saccade paradigm
disjoint with: Reading paradigm
disjoint with: Eating paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A behavioral paradigm in which subjects recall items from episodic memory (autobiographical history, long-term event memories).
has birnlex curator: Angie Laird
has birnlex curator: Jessica Turner
has curation status: uncurated
has external source: BrainMap.org

Difference
type: Class
subclass of: birnlex_11004
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: A quantitative value representing the difference of two underlying quantitative values.

Breathhold paradigm
type: Class
subclass of: Behavioral paradigm
disjoint with: Acupuncture paradigm
disjoint with: Divided auditory attention paradigm
disjoint with: Encoding paradigm
disjoint with: Classical conditioning paradigm
disjoint with: Serial item recognition paradigm
disjoint with: Sensorimotor paradigm
disjoint with: Delayed matching to sample paradigm
disjoint with: Drawing paradigm
disjoint with: Oddball discrimination paradigm
disjoint with: Mismatch negativity paradigm
disjoint with: Deductive reasoning paradigm
disjoint with: Eye Saccade paradigm
disjoint with: Reading paradigm
disjoint with: Eating paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A behavioral paradigm that requires subjects to hold their breath one or more times.
bonfire ID: BF_T0000271
has birnlex curator: Angie Laird
has birnlex curator: Jessica Turner
has curation status: curation complete
has external source: BrainMap.org

TR
type: Class
synonym: MRI repetition time
synonym: Repetition time
definition: The time interval between successive initial excitation pulses in one full playout of a pulse sequence. This is also often used in reference to the time it takes to acquire the entire volume being imaged (e.g., the brain, the ventral surface of the brain).
subclass of: Duration
version info: TODO:
created date: 2007-03-09
modified date: 2007-03-09
modified date: February 9, 2009
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: The amount of time that exists between successive pulse sequences applied to the same slice. It is delineated by initiating the first RF pulse of the sequence then repeating the same RF pulse at a time t. Variations in the value of TR have an important effect on the control of image contrast characteristics. Short values of TR (< 1000 ms) are common in images exhibiting T1 contrast, and long values of TR (> 1500 ms) are common in images exhibiting T2 contrast. TR is also a major factor in total scan time.

Sham control group
type: Class
deprecated: true
subclass of: DeprecatedClass
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A subject group that has received an identical treatment to the experimental group but without the active agent under study.
bonfire ID: BF_T0000148
has former parent class: birnlexInvestigation 174
is replaced by class: birnlex_11045
example: a placebo-treated control group

Functional MRI platform
type: Class
synonym: fMRI platform
subclass of: Magnetic resonance imaging platform
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Acupuncture paradigm
type: Class
subclass of: Behavioral paradigm
disjoint with: Divided auditory attention paradigm
disjoint with: Encoding paradigm
disjoint with: Classical conditioning paradigm
disjoint with: Serial item recognition paradigm
disjoint with: Sensorimotor paradigm
disjoint with: Delayed matching to sample paradigm
disjoint with: Drawing paradigm
disjoint with: Oddball discrimination paradigm
disjoint with: Mismatch negativity paradigm
disjoint with: Deductive reasoning paradigm
disjoint with: Eye Saccade paradigm
disjoint with: Reading paradigm
disjoint with: Eating paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A behavioral paradigm where subjects are stimulated with Chinese acupuncture, a procedure in which thin needles are passed through the skin to specific points.
bonfire ID: BF_T0000339
has birnlex curator: Angie Laird
has birnlex curator: Jessica Turner
has curation status: graph position temporary
has external source: BrainMap.org

Sample dissection
type: Class
subclass of: Specimen preparation
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Divided auditory attention paradigm
type: Class
subclass of: Behavioral paradigm
disjoint with: Encoding paradigm
disjoint with: Classical conditioning paradigm
disjoint with: Serial item recognition paradigm
disjoint with: Sensorimotor paradigm
disjoint with: Delayed matching to sample paradigm
disjoint with: Drawing paradigm
disjoint with: Oddball discrimination paradigm
disjoint with: Mismatch negativity paradigm
disjoint with: Deductive reasoning paradigm
disjoint with: Eye Saccade paradigm
disjoint with: Reading paradigm
disjoint with: Eating paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A behavioral paradigm in which the subject are asked to respond to an auditory stimuli (tone or word discrimination, with or without distractors), during the performance of an unrelated task. Also often co-coded with Tone Monitor/Discrimination.
bonfire ID: BF_T0000347
has birnlex curator: Angie Laird
has birnlex curator: Jessica Turner
has curation status: uncurated
has external source: BrainMap.org

Encoding paradigm
type: Class
subclass of: Behavioral paradigm
disjoint with: Classical conditioning paradigm
disjoint with: Serial item recognition paradigm
disjoint with: Sensorimotor paradigm
disjoint with: Delayed matching to sample paradigm
disjoint with: Drawing paradigm
disjoint with: Oddball discrimination paradigm
disjoint with: Mismatch negativity paradigm
disjoint with: Deductive reasoning paradigm
disjoint with: Eye Saccade paradigm
disjoint with: Reading paradigm
disjoint with: Eating paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A behavioral paradigm in which a subject views stimuli (words, pictures, letters) and are instructed to memorize them.
bonfire ID: BF_T0000358
has birnlex curator: Angie Laird
has birnlex curator: Jessica Turner
has curation status: uncurated
has external source: BrainMap.org

Unit
type: Class
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: Uniform measurement standard used to characterize a quantitative value.

Investigator role
type: Class
deprecated: true
subclass of: DeprecatedClass
created date: 2006-07-15
modified date: 2008-02-21
birnlex definition: Role played by individual investigators during the course of an investigation
has former parent class: OBI 54
is replaced by class: birnlex_11015

Classical conditioning paradigm
type: Class
subclass of: Behavioral paradigm
disjoint with: Serial item recognition paradigm
disjoint with: Sensorimotor paradigm
disjoint with: Delayed matching to sample paradigm
disjoint with: Drawing paradigm
disjoint with: Oddball discrimination paradigm
disjoint with: Mismatch negativity paradigm
disjoint with: Deductive reasoning paradigm
disjoint with: Eye Saccade paradigm
disjoint with: Reading paradigm
disjoint with: Eating paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A behavioral paradigm in which subjects are presented with paired stimuli (usually involving presentation of an eye puff with an auditory tone) in an attempt to study associative learning.
bonfire ID: BF_T0000343
has birnlex curator: Angie Laird
has birnlex curator: Jessica Turner
has curation status: uncurated
has external source: BrainMap.org

Assessment
type: Class
synonym: test
definition: * A procedure for critical evaluation; a means of determining the presence, quality, or truth of something. (NCI) * Administration of tests, and analysis and interpretation of test scores in order to measure differences between individuals or between test performances of the same individual on different occasions. (PSY)
subclass of: birnlex_11022
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: An assessment is the process of evaluating organism attributes via an assessment instrument that results in an assessment measure which may be interpreted in a phenotypical domain.
bonfire ID: BF_T0000276
has birnlex curator: Jessica Turner
has curation status: curation complete
umls cui: C0039593

Tesla
type: Class
synonym: T
subclass of: Unit
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: The preferred unit of magnetic flux density. One tesla is equal to 10,000 gauss. The Tesla unit value is defined as a field strength of 1 Weber per meter 2, where 1 Weber represents 1 x 108 (100,000,000) flux lines. Named after the 20th century, Serbian-American electrical engineer and inventor, Nikola Tesla.

Sham operated control group
type: Class
deprecated: true
subclass of: DeprecatedClass
created date: 2006-06-01
modified date: 2007-08-24
birnlex definition: A subject group that has received an identical surgical procedure to the experimental group but without the treatment under study.
bonfire ID: BF_T0000150
has birnlex curator: Maryann Martone
has curation status: uncurated
has former parent class: birnlexInvestigation 174
is replaced by class: birnlex_11046

Cognitive assessment
type: Class
subclass of: Assessment
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: Jessica Turner
has curation status: uncurated
has external source: UMLS
umls cui: C0870300

Talairach-Tournoux Atlas
type: Class
subclass of: nlx res 090904
version info: 125100
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: A standardized brain atlas published by Talairach and Tournoux.

Genotype
type: Class
subclass of: birnlexLimboClass
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: Bill Bug
has birnlex curator: BIRN OTF
has curation status: definition incomplete
has former parent class: OBI 3

Serial item recognition paradigm
type: Class
subclass of: Item recognition paradigm
disjoint with: Sensorimotor paradigm
disjoint with: Delayed matching to sample paradigm
disjoint with: Drawing paradigm
disjoint with: Oddball discrimination paradigm
disjoint with: Mismatch negativity paradigm
disjoint with: Deductive reasoning paradigm
disjoint with: Eye Saccade paradigm
disjoint with: Reading paradigm
disjoint with: Eating paradigm
change note: moved under the new Item_recognition_paradigm class (BB).
created date: 2006-06-01
modified date: 2006-10-11
acronym: SIRP
birnlex definition: A behavioral paradigm that involves the presentation of sets of target items and the recognition of some of those items vs unfamiliar items presented serially (probe items).
bonfire ID: BF_T0000219
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated

Behavioral assessment
type: Class
subclass of: Assessment
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Verbal fluency assessment
type: Class
subclass of: Cognitive assessment
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: Is an assessment that measures the ability of an individual to name as many items as possible within a specified amount of time. May measure letter (or phonemic, e.g., F-A-S) or category (e.g., animals) fluency.
bonfire ID: BF_T0000225
has birnlex curator: Christine Fennema-Notestine
has curation status: pending final vetting

Monoclonal antibody
type: Class
synonym: Monoclonal
synonym: Monoclonal antibodies
abbrev: mAb
subclass of: Antibody
created date: 2006-05-15
modified date: 2007-03-05
bonfire ID: BF_T0000034
externally sourced definition: An antibody produced by clones of cells such as those isolated after hybridization of activated B lymphocytes with neoplastic cells. These hybrids are often referred to as hybridomas. (MeSH)
has birnlex curator: Maryann Martone
has curation status: uncurated

2D spatial image
type: Class
subclass of: birnlex_11005
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: A type of image where pixel values represent a quantity measure over 2 spatial dimensions.

Confocal microscope
type: Class
subclass of: Optical microscope
created date: 2006-05-15
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Neuropsychological assessment
type: Class
subclass of: Assessment
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: An assessment of neurological function associated with certain behaviors often used in diagnosing brain dysfunction or damage and central nervous system disorders or injury. (adapted from MeSH)
has birnlex curator: Christine Fennema-Notestine
has curation status: uncurated
has external source: UMLS
umls cui: C0027902

Sternberg paradigm
type: Class
synonym: delayed match-to-sample paradigm
subclass of: Item recognition paradigm
editorial note: Brain Map uses this designtation only when letters are used as stimuli; however there is some confusion about whether other stimuli may be used in the Sternberg paradigm
change note: moved under the new Item_recognition_paradigm class (BB).
created date: 2006-06-01
modified date: 2006-10-11
acronym: DMTS
birnlex definition: A delayed matching-to-sample paradigm that uses letters or numbers as stimuli (Sternberg S. High-speed scanning in human memory. Science. 1966 Aug 5;153(736):652-4).
bonfire ID: BF_T0000359
has birnlex curator: Angie Laird
has birnlex curator: Jessica Turner
has curation status: pending final vetting
has external source: BrainMap.org
pending action note: Need to clarify what a Sternberg paradigm involves

Polyclonal antibody
type: Class
synonym: Polyclonal
synonym: Polyclonal antibodies
abbrev: polyAb
subclass of: Antibody
created date: 2006-05-15
modified date: 2007-03-05
bonfire ID: BF_T0000035
externally sourced definition: Immunoglobulins which arise from more than one clone of B-lymphocyte cells. Polyclonal antibodies are usually present when antisera from a conventional immunization is used. (www.brendan.com/Glossary.htm)
has birnlex curator: Maryann Martone
has curation status: uncurated

MRI 3D image
type: Class
subclass of: 3D spatial image
created date: 2007-03-07
modified date: 2007-03-07
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: A type of 3D image collected using an MRI device.

Biochemical specimen preparation protocol
type: Class
subclass of: Specimen preparation protocol
change note: Changed name from the ambiguous Biochemical_protocol to Biochemical_specimen_preparation_protocol (BB).
created date: 2006-06-01
modified date: 2007-03-05
has birnlex curator: Bill Bug
has birnlex curator: BIRN OTF

Laser scanning confocal microscope
type: Class
subclass of: Confocal microscope
created date: 2006-05-15
modified date: 2006-10-11
bonfire ID: BF_T0000022
externally sourced definition: A confocal microscope that that uses a laser that is scanned in a raster pattern across the specimen to excite fluorescence or otherwise visualize the specimen one point at a time. Out of focus light is removed by an aperture inserted in the transmitted light path; 2 or 3 dimensional likenesses are then reconstructed by computer; relatively noninvasive, applicable to thick sections and living tissue. (CSP)
has birnlex curator: Maryann Martone
has curation status: uncurated
has definition source: UMLS defSource

Visual oddball paradigm
type: Class
subclass of: Oddball discrimination paradigm
disjoint with: Auditory oddball paradigm
birnlex definition: An oddball discrimination paradigm where subjects view letters or objects and indicate when they see a target stimulus.
bonfire ID: BF_T0000340
has birnlex curator: Angie Laird
has birnlex curator: Jessica Turner
has curation status: uncurated
has external source: BrainMap.org

Contrast agent
type: Class
subclass of: birnlex_11033
created date: 2006-05-15
modified date: 2007-03-05
externally sourced definition: A chemical substance or formulation regulated as a medical device that is delivered by various routes of administration into the body of a patient undergoing a diagnostic imaging procedure to temporarily enable or enhance the capability of a specified diagnostic imaging. (UMD)
externally sourced definition: Substances used in radiography that allow visualization of certain tissues. (CSP)
externally sourced definition: Substances used in radiography that allow visualization of certain tissues. (MeSH)
has birnlex curator: Bill Bug
has birnlex curator: BIRN OTF
has curation status: uncurated
umls cui: C0009924

Left handedness
type: Class
subclass of: Handedness
created date: 2006-04-04
modified date: 2006-10-11
birnlex definition: A behavioral phenotype where the subject preferentially uses the left hand for tasks requiring the use of a single hand or a dominant hand.
has birnlex curator: Maryann Martone
has curation status: uncurated
has external source: UMLS
umls cui: C0234418

Microscopy contrast enhancement protocol
type: Class
subclass of: Specimen preparation protocol
editorial note: Should really be importing the FlyBase biological imaging ontology, now that it is so mature. Unfortunately, this is currently only available in OBO format. It really needs to be incorporated directly or through import into OBI (BB:2006-10-10).
change note: Changed preferred Label from Contrast_enhancement_protocol to Microscopy_contrast_enhancement_protocol.
created date: 2006-05-15
modified date: 2007-03-05
has birnlex curator: Bill Bug
has birnlex curator: BIRN OTF
has curation status: uncurated
nif ID: _7_6

MRI 2D image
type: Class
subclass of: 2D spatial image
created date: 2007-03-07
modified date: 2007-03-07
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: A type of 2D image collected using an MRI device.

Electron microscope
type: Class
subclass of: Microscope
created date: 2006-05-15
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated
umls cui: C0262879

Ambidextrous
type: Class
subclass of: Handedness
created date: 2006-04-04
modified date: 2006-10-11
birnlex definition: A laterality measure where there is no overall dominance in the use of right or left hand in the performance of tasks that require one hand or a dominant hand.
has birnlex curator: Maryann Martone
has curation status: pending final vetting
has external source: UMLS
umls cui: C0023114

Fixation protocol
type: Class
subclass of: Specimen preparation protocol
editorial note: Should look to FBbi for content here, hopefully brought into BIRNLex-Main via import.
created date: 2006-05-15
modified date: 2007-03-05
has birnlex curator: BIRN OTF
has curation status: uncurated

Scanning electron microscope
type: Class
subclass of: Electron microscope
created date: 2006-05-15
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated
umls cui: C0262878

Cognitive phenotype
type: Class
subclass of: Phenotype
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Immunolabeling protocol
type: Class
subclass of: Specimen preparation protocol
created date: 2006-05-15
modified date: 2007-03-05
has birnlex curator: BIRN OTF
has curation status: uncurated

Sensorimotor paradigm
type: Class
subclass of: Behavioral paradigm
disjoint with: Delayed matching to sample paradigm
disjoint with: Drawing paradigm
disjoint with: Oddball discrimination paradigm
disjoint with: Mismatch negativity paradigm
disjoint with: Deductive reasoning paradigm
disjoint with: Eye Saccade paradigm
disjoint with: Reading paradigm
disjoint with: Eating paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A behavioral paradigm that requires the subject respond to stimuli that are dissimilar to the majority of stimuli presented
bonfire ID: BF_T0000266
has birnlex curator: Jessica Turner
has curation status: curation complete

Transmission electron microscope
type: Class
subclass of: Electron microscope
created date: 2006-05-15
modified date: 2006-10-11
has birnlex curator: Maryann Martone
has curation status: definition incomplete
umls cui: C0262880

Intramuscular injection
type: Class
abbrev: i.m.
subclass of: Injection
disjoint with: Subthelial injection
disjoint with: Intracellular injection
disjoint with: Intraperotineal injection
disjoint with: Intrathecal injection
created date: 2006-06-01
modified date: 2006-10-11
externally sourced definition: administration of a drug via injection into a muscle. (CSP)
externally sourced definition: Forceful administration into a muscle of liquid medication, nutrient, or other fluid through a hollow needle piercing the muscle and any tissue covering it. (MeSH)
has birnlex curator: Bill Bug
has birnlex curator: Maryann Martone
has curation status: uncurated
umls cui: C0021492

Verbal fluency
type: Class
subclass of: Cognitive phenotype
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A cognitive phenotype measuring an individual's facility with producing spoken language.
bonfire ID: BF_T0000225
has birnlex curator: Christine Fennema-Notestine
has curation status: curation complete

Intracellular injection protocol
type: Class
subclass of: Microscopy contrast enhancement protocol
disjoint with: Immunohistochemical protocol
disjoint with: Fluorescence labeling protocol
disjoint with: Immunocytochemistry protocol
disjoint with: Radiolabeling protocol
created date: 2006-05-15
modified date: 2007-03-05
has birnlex curator: BIRN OTF
has curation status: uncurated

Duration
type: Class
subclass of: Temporal characteristic value
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: A type of temporal characteristic value where the time measured is that between the occurance of two events.

Free recall ability
type: Class
deprecated: true
subclass of: DeprecatedClass
created date: 2006-06-01
modified date: 2007-08-24
has birnlex curator: Bill Bug
has birnlex curator: BIRN OTF
has curation status: uncurated
has former parent class: birnlexInvestigation 202

Memory phenotype
type: Class
subclass of: Phenotype
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Staining protocol
type: Class
subclass of: Microscopy contrast enhancement protocol
created date: 2006-05-15
modified date: 2007-03-05
has birnlex curator: BIRN OTF
has curation status: uncurated
nif ID: _7_6.2

Body weight
type: Class
deprecated: true
subclass of: DeprecatedClass
created date: 2006-06-01
modified date: 2007-08-24
birnlex definition: A measure of the mass of the entire body of the organism.
has birnlex curator: Bill Bug
has birnlex curator: BIRN OTF
has curation status: uncurated
has former parent class: birnlexInvestigation 204
umls cui: C0005910

Subthelial injection
type: Class
subclass of: Injection
disjoint with: Intracellular injection
disjoint with: Intraperotineal injection
disjoint with: Intrathecal injection
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: Maryann Martone
has curation status: uncurated

Blood Oxygenation Level Dependent signal
type: Class
synonym: BOLD
subclass of: Difference
created date: 2007-03-09
modified date: 2007-03-09
defining citation: PMID:1948051
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: Haemoglobin is diamagnetic when oxygenated but paramagnetic when deoxygenated. Local changes in the relative concentration of oxyhemoglobin and deoxyhemoglobin and changes in local cerebral blood volume in addition, mean that the magnetic resonance (MR) signal of blood is slightly different depending on the level of oxygenation. Higher BOLD signal intensities arise from decreases in the concentration of deoxygenated hemoglobin since the blood magnetic susceptibility now more closely matches the tissue magnetic susceptibility. (from Wikipedia).

Collaborator
type: Class
subclass of: birnlex_11015
created date: 2006-07-15
modified date: 2007-03-05
birnlex definition: Participant in a research project or experiment, who is not the primary investigator, who performs portions of the research project or who makes significant intellectual contributions to the research project.
bonfire ID: BF_T0000184
has birnlex curator: Maryann Martone
has curation status: uncurated

Organism attribute
type: Class
deprecated: true
subclass of: DeprecatedClass
created date: 2006-06-01
modified date: 2007-08-24
has birnlex curator: Bill Bug
has birnlex curator: BIRN OTF
has curation status: uncurated
has former parent class: birnlexInvestigation 199
pending action note: What is this and how would it differ from Phenotype_attribute (BB)?

Mild cognitive impairment
type: Class
subclass of: Memory phenotype
disjoint with: Working memory phenotype
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: An impairment in cognition, specifically memory performance, that is frequently associated with aging and, in some cases, pre-clinical Alzheimer's disease. The degree and type of impairment distinguishes MCI from dementia in that MCI patients exhibit deficits in tests of memory, but perform normally on standard tests measuring other cognitive domains.
bonfire ID: BF_T0000227
has birnlex curator: Christine Fennema-Notestine
has curation status: uncurated

TA
type: Class
synonym: MRI acquitision time
definition: The time between the initial pulse and the end of the data acquisition. Note that there may be an additional delay placed at the end of the acquisition to achieve a certain repetition time (TR)
subclass of: Duration
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: The time the MRI scanner takes to collect an MRI image.

Sham operated role
type: Class
deprecated: true
subclass of: DeprecatedClass
created date: 2006-06-01
modified date: 2008-02-21
birnlex definition: A subject group that has received an identical surgical procedure to the experimental group but without the treatment under study.
has birnlex curator: Bill Bug
has birnlex curator: Maryann Martone
has curation status: uncurated
has former parent class: birnlex_11018
is replaced by class: birnlex_11046

Physical phenotype
type: Class
subclass of: Phenotype
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Protein expression phenotype
type: Class
subclass of: Molecular phenotype
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Experimental paradigm
type: Class
subclass of: birnlex_11010
created date: 2006-06-01
modified date: 2006-10-11
bonfire ID: BF_T0000261
has birnlex curator: Jessica Turner
has curation status: uncurated

FMRIB Software Library
type: Class
synonym: FSL
subclass of: Software library
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
has former parent class: Software toolkit
temp definition: FSL is a comprehensive library of image analysis and statistical tools for FMRI, MRI and DTI brain imaging data (http://www.fmrib.ox.ac.uk/fsl/).

Project leader
type: Class
subclass of: birnlex_11015
created date: 2006-07-15
modified date: 2007-03-05
birnlex definition: Participant in a research project, who may or may not be the principal investigator, who assumes the responsiblity for completion of a project. Responsibilities may include research design, performance of experiments or supervision of other experimenters and communication of results.
bonfire ID: BF_T0000183
has birnlex curator: Maryann Martone
has curation status: uncurated

Dynamic causal modeling
type: Class
abbrev: DCM
subclass of: birnlex_11008
created date: 2007-03-07
modified date: 2007-03-07
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: Dynamic Causal Modeling: As published by Friston, Harrison, and Penny (Neuroimage, 2003, 19, 1273-1302), this is a method for "identifying non-linear input-state-output systems", as applied to determining effective connectivity in fMRI data. The emphasis is on determining the effects of the experimental inputs on the coupling or co-activations of various brain regions (psychophysiological interactions), rather than the effects of the experimental inputs on the activation of each brain region separately.

TE
type: Class
synonym: Echo time
synonym: MRI echo time
definition: The time interval between excitation and data acquisition of the center of k-space. This is also referred to as echo time and typically measured in units of milliseconds. (Huettel, Song, & McCarthy, 2004).
subclass of: Duration
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: This is an imaging parameter which helps determine image contrast. It represents the time in milliseconds between the application of the 90degree pulse and the peak of the echo signal in Spin Echo and Inversion Recovery pulse sequences

Working memory phenotype
type: Class
subclass of: Memory phenotype
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Gender phenotype
type: Class
subclass of: Physical phenotype
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: The observable physical characteristics typical of the male or female of the species.
has birnlex curator: Maryann Martone
has curation status: uncurated

Organism characteristic
type: Class
deprecated: true
subclass of: DeprecatedClass
created date: 2006-07-15
modified date: 2007-03-05
has former parent class: OBI 3

Experimenter
type: Class
subclass of: birnlex_11015
created date: 2006-07-15
modified date: 2007-03-05
has birnlex curator: Maryann Martone
has curation status: uncurated

Behavioral paradigm
type: Class
subclass of: Experimental paradigm
editorial note: This list contains terms from Brain Map and BIRN; right now it is presented as a fairly flat list of paradigms. Functional classifications were deliberately avoided. This list contains many pre-coordinated terms which will be reconsidered in the future (JT).
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: In the behavioural sciences, e.g. Psychology, Biology, Neurosciences, an experimental paradigm is an experimental setup (i.e. a way to conduct a certain type of experiment) that is defined by certain fine-tuned standards and often has a theoretical background. Within an Experimental Paradigm, the behavioral paradigm describes the behavioral aspects of the experiment: what stimuli are presented to the subject when, and under what conditions, and what the subject's responses are supposed to be.
bonfire ID: BF_T0000262
has birnlex curator: Angie Laird
has birnlex curator: Jessica Turner
has curation status: definition incomplete
has curation status: graph position temporary
has external source: BrainMap.org

Gene specific probe
type: Class
subclass of: birnlex_11033
created date: 2006-05-15
modified date: June 25, 2009
has birnlex curator: BIRN OTF
has curation status: uncurated
has former parent class: birnlex_11020

Reagent
type: Class
deprecated: true
subclass of: DeprecatedClass
created date: 2006-05-15
modified date: 2007-03-05
externally sourced definition: Substances intended to detect and/or measure, in some cases producing or modifying other substances, a specific analyte of interest (e.g., enzymes, hormones). Substances used as reagents must be sufficiently pure to appropriately perform a specific analytical test. Reagents are typically used in the clinical laboratory for clinical chemistry, immunochemistry, hematology, microbiology (e.g., culture), infectious immunology, and molecular biology (e.g., nucleic acid technology) tests. (UMD)
has birnlex curator: BIRN OTF
has curation status: uncurated
has former parent class: OBI 258
is replaced by class: birnlex_11019
umls cui: C0034760

Polynomial coefficient
type: Class
synonym: proportionality coefficient
synonym: scaling coefficient
subclass of: birnlex_11004
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: A scaling factor applied to a given independent variable in a polynomial equation. Such characteristic values are often linked to physical significant proporties of real-world systems that are modeled by polynomial equations.

AFNI
type: Class
subclass of: Software toolkit
created date: 2007-03-07
modified date: 2007-03-07
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: AFNI (which might be an acronym for Analyis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X (http://afni.nimh.nih.gov/afni/).

Vector
type: Class
subclass of: birnlex_11004
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: An n-dimensional quantity representing a value that has both an amplitude and a direction. A vector quantity can have 1 or more dimensions. The overall amplitude of a multi-dimensional vector quantity is the square-root of the sum of the sqaures of the amplitudes in each individual dimension.

Molecular phenotype
type: Class
subclass of: Phenotype
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Protein specific probe
type: Class
subclass of: birnlex_11033
disjoint with: DNA specific probe
disjoint with: RNA specific probe
created date: 2006-05-15
has birnlex curator: BIRN OTF
has curation status: uncurated
has former parent class: birnlex_11020

Item recognition paradigm
type: Class
subclass of: Behavioral paradigm
created date: 2006-10-11
modified date: 2006-10-11
birnlex definition: A behavioral paradigm where sets of target items are presented at the outset and the recognition of one or more of those items vs unfamiliar items is tested using a probe item.
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: pending final vetting

Algorithm
type: Class
deprecated: true
subclass of: DeprecatedClass
created date: 2006-06-01
modified date: 2007-03-05
birnlex definition: A well defined set of rules that can be expressed using formal mathematical expression and thereby implemented in a computing environment.
has birnlex curator: Bill Bug
has birnlex curator: Brett Peterson
has curation status: curation complete
has external source: UMLS
has former parent class: OBI 5
is replaced by class: birnlex_11009
umls cui: C0002045

Institution
type: Class
subclass of: BFO_0000027
change note: This had been subclassed previously from the obi:independent_continuant, which has since been subsumed into bfo:independent_continuant. Just as with Experiment, it is not appropriate to have something as concrete as a participating research institution so high up in the more abstract layers of the ontology. I think it can live here under bfo:object_aggregate for now and possibly even stay here (BB:2006-10-10).
created date: 2006-04-04
modified date: 2006-10-11
birnlex definition: The organization to which an individual researcher or groups of researchers belong and where the research is usually conducted, usually a university or medical facility.
has birnlex curator: Bill Bug
has birnlex curator: Maryann Martone
has curation status: graph position temporary
pending action note: Check with BFO researchers whether this is an appropriate location in BFO for this class. Institutions are definitely entities they've had to handle before.

Phenotype
type: Class
subclass of: birnlexLimboClass
editorial note: How does this related to Phenotype_attribute and to PaTO expressions (BB)?
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: Bill Bug
has birnlex curator: BIRN OTF
has curation status: uncurated
has former parent class: birnlexMain_7

Delayed matching to sample paradigm
type: Class
subclass of: Behavioral paradigm
disjoint with: Drawing paradigm
disjoint with: Oddball discrimination paradigm
disjoint with: Mismatch negativity paradigm
disjoint with: Deductive reasoning paradigm
disjoint with: Eye Saccade paradigm
disjoint with: Reading paradigm
disjoint with: Eating paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A behavioral paradigm in which subjects view three or more items.. After a brief delay a probe item is presented and subjects are asked to recall if the probe item was presented in the the previous list. Stimuli can be words, pictures, or abstract patterns. If the stimuli are letters, the task is coded as a Sternberg Task.
bonfire ID: BF_T0000346
has birnlex curator: Angie Laird
has birnlex curator: Jessica Turner
has curation status: uncurated
has external source: BrainMap.org

DNA specific probe
type: Class
subclass of: Gene specific probe
disjoint with: RNA specific probe
created date: 2006-05-15
modified date: 2007-03-05
has birnlex curator: BIRN OTF
has curation status: uncurated

Lead institution
type: Class
subclass of: Institution
created date: 2006-04-04
modified date: 2006-10-11
has birnlex curator: Bill Bug
has birnlex curator: Maryann Martone
has curation status: graph position temporary

Transmission electron microscopic imaging assay
type: Class
subclass of: Microscopic imaging assay
created date: 2006-05-15
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has birnlex curator: Maryann Martone
has curation status: uncurated

Cardinal part of imaging instrument
type: Class
subclass of: birnlex_11029
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Imaging instrument
type: Class
subclass of: birnlex_11035
created date: 2006-05-15
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Behavioral phenotype
type: Class
subclass of: Phenotype
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Collaborating institution
type: Class
subclass of: Institution
created date: 2006-04-04
modified date: 2006-10-11
has birnlex curator: Bill Bug
has birnlex curator: Maryann Martone
has curation status: graph position temporary

RNA specific probe
type: Class
subclass of: Gene specific probe
created date: 2006-05-15
modified date: 2007-03-05
has birnlex curator: BIRN OTF
has curation status: uncurated

Cardinal part of microscope
type: Class
subclass of: Cardinal part of imaging instrument
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Magnetic resonance imaging scanner
type: Class
synonym: MRI scanner
subclass of: Imaging instrument
created date: 2006-05-15
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Relaxation time
type: Class
subclass of: Temporal characteristic value
editorial note: We may want to eventually include the 1/e mathematical definition of relaxation time.
created date: 2007-03-07
modified date: 2007-03-07
has birnlex curator: BIRN OTF
has curation status: uncurated
temp definition: a type of temporal characteristic value where the time measured is that required to return to an equilibrium state following a well-defined stimulus.

Smoking behavior
type: Class
subclass of: Behavioral phenotype
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Toxin
type: Class
deprecated: true
subclass of: DeprecatedClass
created date: 2006-05-15
modified date: 2007-03-05
birnlex definition: A probe for identifying macromolecules that is a specific, characterizable, poisonous chemical, often a protein, with specific biological properties, produced by microbes, higher plants, or animals, that react with specific components of cells or tissues.
has birnlex curator: Maryann Martone
has curation status: uncurated
is replaced by class: birnlex 2103 2
umls cui: C0040549

Trail making test
type: Class
subclass of: Neuropsychological assessment
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: Is a neuropsychological assessment of conceptual abilities and visuo-motor sequencing. Part A measures subjects ability to draw lines to connect consecutively numbered circles on a work sheet. Part B measures subjects draw lines between consecutively numbered and lettered circles by alternating between the two sequences (e.g., 1-A-2-B-3-C ...).
bonfire ID: BF_T0000223
has birnlex curator: Christine Fennema-Notestine
has curation status: curation complete

Microscope
type: Class
subclass of: Imaging instrument
created date: 2006-05-15
modified date: 2006-10-11
birnlex definition: An instrument used to obtain a magnified image of small objects and reveal details of structure not otherwise distinguishable.
has birnlex curator: BIRN OTF
has curation status: uncurated
has external source: UMLS
umls cui: C0181839

Staining
type: Class
definition: Used in various techniques, staining is the artificial coloration of a substance that enhances the contrast of tissues, genes, cells, or microorganisms(etc.), to be viewed under the microscope. In biochemistry it involves adding a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound. Staining can serve the same purpose as fluorescent tagging. (Adapted from Wikipedia)
subclass of: Specimen preparation
editorial note: BIRNLex should make use of OBO Flybase bioimaging (FBbi ontology) (see the EBI Ontology Browser), once it is available in OWL. Though we could use the OBO to OWL converts, this is problematic.
created date: 2006-06-01
modified date: 2006-10-11
modified date: October 29, 2010
has birnlex curator: Bill Bug
has birnlex curator: BIRN OTF
has curation status: uncurated

T1 relaxation time
type: Class
synonym: Spin-lattice relaxation time
subclass of: Relaxation time
editorial note: We may want to eventually include the 1/e mathematical definition of relaxation time.
created date: 2007-03-07
modified date: 2007-03-07
modified date: February 9, 2009
has birnlex curator: BIRN OTF
has curation status: uncurated
temp definition: a type of temporal characteristic value where the time meansured is the time required to return to an equilibrium state following a well-defined external stimulus.

Smoking
type: Class
subclass of: Smoking behavior
disjoint with: Past smoking behavior
disjoint with: Non smoking
disjoint with: Never has smoked
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: Behavioral phenotype used to describe an individual who currently smokes tobacco products.
has birnlex curator: Jessica Turner
has curation status: pending final vetting
umls cui: C0337664

Antibody
type: Class
synonym: antibodies
abbrev: Ab
subclass of: Protein specific probe
created date: 2006-05-15
modified date: 2007-03-05
birnlex definition: Immunoglobulin that is used as a reagent to localize a signal through an immunological reaction.
bonfire ID: BF_T0000132
has birnlex curator: Maryann Martone
has curation status: uncurated
example: antibody used for immunocytochemical protocol

Mini mental state examination
type: Class
subclass of: Neuropsychological assessment
created date: 2006-06-01
modified date: 2006-10-11
acronym: MMSE
birnlex definition: Is a neuropsychological assessment of cognitive function that is a widely used for measuring cognitive impairment. Developed in 1975 by Marshall Folstein and his colleagues (Citation)
bonfire ID: BF_T0000222
has birnlex curator: Christine Fennema-Notestine
has curation status: definition incomplete

Optical microscope
type: Class
subclass of: Microscope
created date: 2006-05-15
modified date: 2006-10-11
bonfire ID: ssss
has birnlex curator: BIRN OTF
has curation status: uncurated

Past smoking behavior
type: Class
synonym: ex smoking behavior
synonym: former smoking behavior
subclass of: Smoking behavior
disjoint with: Non smoking
disjoint with: Never has smoked
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A behavioral phenotype used to describe an individual who is currently not smoking tobacco products but has at some time in the past.
has birnlex curator: BIRN OTF
has curation status: pending final vetting
umls cui: C0337671

Anatomical atlas data set
type: Class
deprecated: true
synonym: Atlas
subclass of: DeprecatedClass
editorial note: May have to adapt this definition or alter class to reflect that fact some atlases are collections of data sets.
created date: 2007-03-07
modified date: March 31, 2009
has birnlex curator: BIRN OTF
has curation status: uncurated
has former parent class: Anatomical data set
nif ID: _1_1.2
temp definition: A type of anatomical data set contains a collection of anatomical maps.
example: ABA C57Bl/6 Adult Mouse Brain Atlas
example: AMA atlas of the body
example: Franklin-Paxinos C57Bl/6J Adult Mouse Brain Atlas in stereotaxic coordinates (2001).
example: LONI Minimum Deformation C57Bl/6 Mouse Brain Atlas
example: MNI Atlas
example: NeuroTerrain C57Bl/6 Adult Mouse Brain Atlas
example: Talairach-Tournoux Atlas
example: Yale atlas of echocardiography
scope note: GENSAT is an image data set but not a map, and, therefore, not an atlas data set. Query Atlas and SMART Atlas are tools that use atlas data sets.

Phalloidin
type: Class
deprecated: true
subclass of: DeprecatedClass
created date: 2006-05-15
modified date: 2007-03-05
externally sourced definition: Phalloidin is a toxin from the Death Cap mushroom that binds actin, inhibiting its depolymerization. Phalloidin binds specifically F-actin and is therefore a very convenient tool to investigate the distribution of F-actin since fluorescent analogs can be synthesized that retain actin binding. (Wikipedia)
has birnlex curator: Maryann Martone
has curation status: uncurated
has external source: UMLS
is replaced by class: CHEBI 8040
umls cui: C0031312

Multiphoton microscope
type: Class
synonym: Multi-photon microscope
subclass of: Optical microscope
change note: Definition Modified (December 23, 2008)
created date: 2006-05-15
modified date: 2007-10-11
modified date: December 23, 2008
birnlex definition: Optical microscope with a multiphoton attachment, where fluorescence excitation is produced by two or more photons of light of longer wavelength that the fluorophore. On their own, these photons possess insufficient energy to excite the fluorophore but under certain conditions, the two photons can interact to produce excitation in a narrow focal plane.
bonfire ID: BF_T0000028
has birnlex curator: Maryann Martone
has curation status: uncurated

Experiment
type: Class
subclass of: BFO_0000015
editorial note: Not sure whether this is the same as study; needs clarification (MM).
change note: Moved this to bfo:process. It was formerly a subclass of occurrent, which is too deep in the hierarchy for an object as concrete as an experiment. We need to determine how to use the study & investigation classes from OBI under bfo:process (BB).
created date: 2006-04-04
modified date: 2006-10-11
birnlex definition: A set of actions and observations, performed to verify or falsify a hypothesis or research a causal relationship between phenomena. The experiment is a cornerstone in empirical approach to knowledge. (adapted from wikipedia.org)
bonfire ID: BF_T0000189
has birnlex curator: Bill Bug
has birnlex curator: BIRN OTF
has birnlex curator: Maryann Martone
has curation status: pending final vetting
history note: The original BIRNLex had its own occurrent class called "Evolves through time". This was subsumbed into fugo:occurrent, which itself has now been subsumed into bfo:occurrent.

T2 weighted 2D image
type: Class
subclass of: MRI 2D image
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: A type of 2D MRI image collected using an T2 Weighted MRI imaging protocol.

Anatomical data set
type: Class
deprecated: true
subclass of: DeprecatedClass
created date: 2007-03-07
modified date: 2007-03-07
has birnlex curator: BIRN OTF
has curation status: uncurated
has former parent class: birnlex_11006
temp definition: A type of data set describing anatomical objects.

Non smoking
type: Class
subclass of: Smoking behavior
disjoint with: Never has smoked
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: Behavioral phenotype used to describe an individual who does not currently smoke tobaccor products. This term describes only current behavior and does not imply that the individual never smoked.
has birnlex curator: BIRN OTF
has curation status: pending final vetting
has external source: UMLS
umls cui: C0337672

Digital aggregate entity
type: Class
subclass of: BFO_0000031
created date: 2007-03-07
modified date: 2007-03-07
has birnlex curator: Bill Bug
has curation status: uncurated

Block design
type: Class
synonym: Box_car_design
subclass of: birnlex_11008
created date: 2007-03-07
modified date: 2007-03-07
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: An experimental design in which conditions of interest are continued for up to 30 s, and the time course is modeled as a constant state during those "blocks" of time.

Specimen preparation protocol
type: Class
subclass of: birnlex_11010
created date: 2006-05-15
modified date: 2007-03-05
has birnlex curator: Bill Bug
has birnlex curator: BIRN OTF
has curation status: uncurated
umls cui: C0200363

Agent delivery process
type: Class
subclass of: BFO_0000015
created date: 2006-05-15
modified date: 2006-10-11
birnlex definition: The process by which an experimental agent is delivered to an organism or part of organism.
bonfire ID: BF_T0000274
has birnlex curator: Maryann Martone
has curation status: curation complete
example: ingestion of toxin
example: injection of drug

MNI Atlas
type: Class
subclass of: nlx res 090904
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: A standardized brain atlas developed by the Montreal Neurological Institute.

Imaging protocol
type: Class
subclass of: birnlex_11010
created date: 2007-03-07
modified date: 2007-03-07
has birnlex curator: BIRN OTF
has curation status: uncurated

fMRI beta
type: Class
synonym: BETA
subclass of: Polynomial coefficient
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: in fMRI results, the coefficient from the General Linear Model which reflects the strength of the relationship between the data and the modeled effect. Usually one beta value per voxel per modeled effect.

Ingestion
type: Class
subclass of: Agent delivery process
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: Bill Bug
has birnlex curator: Maryann Martone
has curation status: uncurated
umls cui: C0232478

Convolution
type: Class
subclass of: birnlex_11009
created date: 2007-03-07
modified date: 2007-03-07
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: A mathematical operation that describes the action of a linear system on a signal.
example: For fMRI, the time course of an experimental design's conditions beginning and ending is often convolved with the Hemodynamic Response Function (HRF) to model fMRI data.

Vascular perfusion
type: Class
subclass of: Agent delivery process
editorial note: This BONFIRE ID is actually from vascular perfusion fixation, but I think this entity should be listed under agent delivery process rather than as a type of fixation (MM).
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: Method of agent delivery where the agent is pumped through the vasculature of the animal.
bonfire ID: BF_T0000032
has birnlex curator: Maryann Martone
has curation status: uncurated

Immersion
type: Class
subclass of: Agent delivery process
created date: 2006-06-02
modified date: 2006-10-11
birnlex definition: A process for delivering an agent to an object of study in which the object is physically submersed in the agent.
has birnlex curator: Maryann Martone
has curation status: uncurated
has external source: UMLS
umls cui: C0020940
example: immersion of a tissue sample into fixative

Preparative role
type: Class
subclass of: birnlex_11019
created date: 2007-03-05
modified date: 2007-03-05
birnlex definition: A role played by a continuant in an investigational protocol designed to prepare a Biomaterial_entity for experimental manipulation.
has birnlex curator: Bill Bug
has curation status: graph position temporary

Gene expression phenotype
type: Class
subclass of: Molecular phenotype
created date: 2006-06-01
modified date: 2006-10-11
bonfire ID: nnnnnn
has birnlex curator: BIRN OTF
has curation status: uncurated

T1 weighted protocol
type: Class
synonym: T1 weighted scan
definition: An MRI scanning pulse sequence that is used to acquire structural data whose tissue contrast parameter is T1-weighted.
subclass of: Anatomical MRI protocol
editorial note: definition mtd, modified from kgh's other anatomical definitions.
created date: 2007-03-07
modified date: February 5, 2009
has birnlex curator: BIRN OTF
has curation status: uncurated
temp definition: An imaging protocol typically using short TE and TR times whose contrast and brightness are predominately determined by T1 signals. This leads to high contrast between white and gray matter and is the basis for high-resolution anatomical brain imaging.

Injection
type: Class
subclass of: Agent delivery process
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: Maryann Martone
has curation status: uncurated
umls cui: C0021485

Intracellular injection
type: Class
subclass of: Injection
disjoint with: Intraperotineal injection
disjoint with: Intrathecal injection
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: Injection of a dye or some other indicator agent into a cell using a micropipette to delineate cell morphology or the distribution of a signal across a single cell. May be in fixed or live tissue.
bonfire ID: BF_T0000117
has birnlex curator: Maryann Martone
has curation status: uncurated

Instrument operator
type: Class
subclass of: birnlex_11015
created date: 2006-07-15
modified date: 2007-03-05
has birnlex curator: Maryann Martone
has curation status: uncurated

Fixative
type: Class
subclass of: Preparative role
created date: 2006-05-15
modified date: 2006-10-11
externally sourced definition: Agents employed in the preparation of histologic or pathologic specimens for the purpose of maintaining the existing form and structure of all of the constituent elements. Great numbers of different agents are used; some are also decalcifying and hardening agents. They must quickly kill and coagulate living tissue. (MeSH)
externally sourced definition: Reagents used for coagulation and/or precipitation of protoplasmatic substances (i.e., fixation), making them resistant to further changes either from the reagents to which they are subjected or from autolysis and putrefaction before microscopic sections can be prepared. Several substances are used as fixatives, including formaldehyde, mercury chloride, and glutaraldehyde solutions; some include decalcifier additives. (UMD)
has birnlex curator: BIRN OTF
has curation status: uncurated
umls cui: C0016184

T2 relaxation time
type: Class
synonym: Spin-spin relaxation time
synonym: Transverse relaxation time
subclass of: Relaxation time
editorial note: Is transverse relaxation time truly a synonym for this entity under all conditions (BB: 2007-03-09)?
editorial note: We may want to eventually include the 1/e mathematical definition of relaxation time.
created date: 2007-03-09
modified date: 2007-03-09
modified date: February 9, 2009
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: Spin-spin or transverse relaxation time. The time constant for loss of phase coherence among spins oriented at an angle to the static magnetic field due to interactions between the spins. Results in a loss of transverse magnetization and the MRI signal.
temp definition: The time constant, T2, which determines the rate at which excited protons reach equilibrium, or go out of phase with each other. A measure of the time taken for spinning protons to lose phase coherence among the nuclei spinning perpendicular to the main field due to interaction between spins, resulting in a reduction in the transverse magnetization. The transverse magnetization value will drop from maximum to a value of about 37% of its original value in a time of T2.

Microscopic imaging assay
type: Class
subclass of: birnlex_11026
created date: 2006-05-15
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Quantitative organism attribute
type: Class
deprecated: true
subclass of: DeprecatedClass
change note: Changed name to singular from plural to comply with univocity constraint (BB).
created date: 2006-06-01
modified date: 2007-08-24
has birnlex curator: Bill Bug
has birnlex curator: BIRN OTF
has curation status: definition incomplete
has former parent class: birnlexInvestigation 199

Drawing paradigm
type: Class
subclass of: Behavioral paradigm
disjoint with: Oddball discrimination paradigm
disjoint with: Mismatch negativity paradigm
disjoint with: Deductive reasoning paradigm
disjoint with: Eye Saccade paradigm
disjoint with: Reading paradigm
disjoint with: Eating paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A behavioral paradigm in which the subject is asked to draw lines, circles or more complex figures using a pen or stylus.
bonfire ID: BF_T0000356
has birnlex curator: Angie Laird
has birnlex curator: Jessica Turner
has curation status: uncurated
has external source: BrainMap.org

Glutaraldehyde fixative
type: Class
synonym: glutaral
synonym: glutardialdehyde
synonym: pentanedial
subclass of: Fixative
created date: 2006-05-15
modified date: 2007-03-05
birnlex definition: A crosslinking fixative. Glutaraldehdye is a pentanedial; 5-carbon saturated chain with a highly reactive aldehyde group on each end (MM).
externally sourced definition: A general purpose reagent is a chemical reagent that has general laboratory application, that is used to collect, prepare, and examine specimens from the human body for diagnostic histopathology, cytology, and hematology, and that is not labeled or otherwise intended for a specific diagnostic application. General purpose reagents include cytological preservatives, decalcifying reagents, fixatives and adhesives, tissue processing reagents, isotonic solutions, and pH buffers. (SPN)
externally sourced definition: One of the protein CROSS-LINKING REAGENTS that is used as a disinfectant for sterilization of heat-sensitive equipment and as a laboratory reagent, especially as a fixative. (MSH)
externally sourced definition: pentanedial; 5-carbon saturated chain with a highly reactive aldehyde group on each end; used as a protein crosslinking agent, fixative, disinfectant, and mutagen. (CSP)
has birnlex curator: Bill Bug
has birnlex curator: Maryann Martone
has curation status: graph position temporary
pending action note: This is a placeholder for a ChEBI class (BB: 2007-03-05).
umls cui: C0017814

Intraperotineal injection
type: Class
abbrev: i.p.
subclass of: Injection
disjoint with: Intrathecal injection
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: Maryann Martone
has curation status: uncurated

T2* relaxation time
type: Class
synonym: T-two-star
subclass of: Relaxation time
editorial note: We may want to eventually include the 1/e mathematical definition of relaxation time.
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: The time constant for loss of phase coherence among spins oriented at an angle to the static magnetic field due to a combination of magnetic field inhomogeneities and the spin-spin relaxation. Results in a rapid loss of transverse magnetization and the MRI signal.T2* < T2. This is the basis for EPI and thus fMRI.

Data analyzer
type: Class
subclass of: birnlex_11015
created date: 2006-07-15
modified date: 2007-03-05
has birnlex curator: Maryann Martone
has curation status: uncurated

Light microscopic imaging assay
type: Class
subclass of: Microscopic imaging assay
created date: 2006-05-15
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Phenotype attribute
type: Class
deprecated: true
subclass of: DeprecatedClass
editorial note: What organism characteristic could not be described as a phenotype attribute? (Age). How does this relate to PaTO? Will instances of this class include PaTO expressions? If so, and given that PaTO expressions include qualities, this appears to be a circular class - well, not quite circular, but probably inappropriate. PaTO expressions will be used to describe instances in data repositories and will include pointers to classes in BIRNLex.(BB).
created date: 2006-06-01
modified date: 2007-08-24
has birnlex curator: Bill Bug
has birnlex curator: BIRN OTF
has curation status: uncurated
has former parent class: birnlexInvestigation 199

Specimen fixation
type: Class
subclass of: birnlex_11023
created date: 2006-07-15
modified date: 2006-07-15
bonfire ID: BF_T0000236
externally sourced definition: The technique of using FIXATIVES in the preparation of cytologic, histologic, or pathologic specimens for the purpose of maintaining the existing form and structure of all the constituent elements. (MeSH)
has birnlex curator: Maryann Martone
has curation status: pending final vetting
has definition source: MeSH defSource

Intrathecal injection
type: Class
subclass of: Injection
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: Maryann Martone
has curation status: uncurated
umls cui: C0021896

Tannic acid fixative
type: Class
subclass of: Fixative
created date: 2006-05-15
modified date: 2007-03-05
externally sourced definition: A fixative and contrast agent which is a lustrous powder, yellow to light-brown in color, that is found in tree bark (particularly oak), fruits, leaves, and tea. It is used medicinally as an astringent, commercially in tanning hides, and as a dye mordant. (Saunders Dictionary and Encyclopedia of Laboratory Medicine and Technology, 1984).
externally sourced definition: A lustrous powder, yellow to light-brown in color, that is found in tree bark (particularly oak), fruits, leaves, and tea. It is used medicinally as an astringent, commercially in tanning hides, and as a dye mordant. (Saunders Dictionary and Encyclopedia of Laboratory Medicine and Technology, 1984). It is also used as a histological fixative and stain. (MeSH)
has birnlex curator: Maryann Martone
has curation status: graph position temporary
has external source: UMLS
pending action note: This is a placeholder for a ChEBI class (BB: 2007-03-05).
umls cui: C0039294

Principal investigator
type: Class
subclass of: birnlex_11015
created date: 2006-07-15
modified date: 2007-03-05
birnlex definition: Participant in a research project who directs a research project or program. The principal investigator (the PI) usually writes and submits the grant application, oversees the scientific and technical aspects of the grant, and has responsibility for the management of the research. www.medterms.com
bonfire ID: BF_T0000157
has birnlex curator: Maryann Martone
has curation status: uncurated

Electron microscopic imaging assay
type: Class
subclass of: Microscopic imaging assay
created date: 2006-05-15
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has birnlex curator: Maryann Martone
has curation status: uncurated

Tissue dissection
type: Class
subclass of: birnlex_11023
created date: 2006-05-15
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Paraformaldehyde fixative
type: Class
subclass of: Fixative
created date: 2006-05-15
modified date: 2007-03-05
birnlex definition: A cross linking fixative consisting of a very low molecular weight polymer of formaldehyde, or a mixture of polyoxymethylene glycols, in the form of a white solid which easily depolymerizes by heating to yield formaldehyde gas and water vapor. Often used by histologists to refer to formaldehyde that has been prepared freshly from paraformaldehyde (MM).
externally sourced definition: A general purpose reagent is a chemical reagent that has general laboratory application, that is used to collect, prepare, and examine specimens from the human body for diagnostic histopathology, cytology, and hematology, and that is not labeled or otherwise intended for a specific diagnostic application. General purpose reagents include cytological preservatives, decalcifying reagents, fixatives and adhesives, tissue processing reagents, isotonic solutions, and pH buffers. (SPN)
has birnlex curator: Bill Bug
has birnlex curator: Maryann Martone
has curation status: uncurated
has external source: UMLS
pending action note: This is a placeholder for a ChEBI class (BB: 2007-03-05).
umls cui: C0070066

Tissue sectioning
type: Class
subclass of: Tissue dissection
created date: 2006-05-15
modified date: 2006-10-11
has birnlex curator: Maryann Martone
has curation status: uncurated

Nicotine use assessment
type: Class
subclass of: Behavioral assessment
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Energy filter
type: Class
subclass of: Cardinal part of microscope
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Fagerstrom test for nicotine dependence
type: Class
subclass of: Nicotine use assessment
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: is an assessment which consists of a questionnaire that measures nicotine use (Fagerstrom citation)
has birnlex curator: Jessica Turner
has curation status: uncurated
umls cui: C0451156

Gross dissection
type: Class
subclass of: Tissue dissection
created date: 2006-05-15
modified date: 2006-10-11
has birnlex curator: Maryann Martone
has curation status: uncurated

Auditory oddball paradigm
type: Class
subclass of: Oddball discrimination paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: An oddball discrimination paradigm that involves responding to auditory stimuli that are dissimilar to the majority of auditory stimuli presented.
has birnlex curator: Jessica Turner
has curation status: curation complete

California Verbal Learning Test
type: Class
subclass of: Neuropsychological assessment
created date: 2006-06-01
modified date: 2006-10-11
bonfire ID: BF_T0000220
has birnlex curator: BIRN OTF
has curation status: definition incomplete

Microdissection
type: Class
subclass of: Tissue dissection
created date: 2006-05-15
modified date: 2006-10-11
has birnlex curator: Maryann Martone
has curation status: uncurated
umls cui: C0598304

In column energy filter
type: Class
subclass of: Energy filter
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

3D spatial image
type: Class
subclass of: birnlex_11005
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: A type of image where pixel values represent a quantity measure over 3 spatial dimensions.

Simple saccade paradigm
type: Class
subclass of: Eye Saccade paradigm
disjoint with: Anti saccade paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A behavioral paradigm in which a subject fixate on a target and are instructed to make a saccadic eye movement to a stimulus (modified from Brain Map by OTF)
has birnlex curator: Angie Laird
has birnlex curator: BIRN OTF
has birnlex curator: Jessica Turner
has curation status: pending final vetting
has external source: BrainMap.org
scope note: This term is equivalent to "saccade paradigm" in Brain Map

Never has smoked
type: Class
subclass of: Smoking behavior
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: Behavioral phenotype used to describe an individual who has never smoked tobacco products.
has birnlex curator: BIRN OTF
has curation status: uncurated

Laser capture
type: Class
subclass of: Microdissection
created date: 2006-05-15
modified date: 2006-10-11
externally sourced definition: method for procuring pure cells from specific microscopic regions of tissue sections; laser beam focally activates a special transfer film which bonds specifically to cells identified and targeted by microscopy within the tissue section, when the film is removed, the chosen cells are tightly held within the focally expanded polymer for microdissection. (CSP)
has birnlex curator: Maryann Martone
has curation status: uncurated
umls cui: C1113652

Tissue section
type: Class
subclass of: birnlex_11027
created date: 2006-05-15
modified date: 2006-10-11
birnlex definition: A sample of a specimen consisting of a thin plane produced through the use of a microtome or other cutting device, usually produced for the purposes of histological processing and/or microscopic examination.
bonfire ID: BF_T0000134
has birnlex curator: Maryann Martone
has curation status: uncurated

T1 weighted 2D image
type: Class
subclass of: MRI 2D image
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: A type of 2D MRI image collected using an T1 Weighted MRI imaging protocol.

PET imaging protocol
type: Class
synonym: Positron Emission Tomography imaging protocol
definition: * A technique for measuring the gamma radiation produced by collisions of electrons and positrons (anti-electrons) within living tissue. In positron emission tomography (PET), a subject is given a dose of a positron-emitting radionuclide attached to a metabolically active substance (for example, 2-fluoro-2-deoxy-D-glucose (FDG), which is similar to a naturally occurring sugar, glucose, with the addition of a radioactive fluorine atom). When living tissue containing the positron emitter is bombarded by electrons, gamma radiation produced by collisions of electrons and positrons is detected by a scanner, revealing in fine detail the tissue location of the metabolically-active substance administered. (NCI04) (NCI) * An imaging technique using compounds labelled with short-lived positron-emitting radionuclides (such as carbon-11, nitrogen-13, oxygen-15 and fluorine-18) to measure cell metabolism. It has been useful in study of soft tissues such as CANCER; CARDIOVASCULAR SYSTEM; and BRAIN. SPECT is closely related to PET, but uses isotopes with longer half-lives and resolution is lower. (MSH) * For this type of scan, a person is given a substance that reacts with tissues in the body to release protons (parts of an atom). Through measuring the different amounts of protons released by healthy and cancerous tissues, a computer creates a picture of the inside of the body. PET images show the chemical functioning of an organ or tissue, unlike X-ray, CT, or MRI which show only body structure. Also called PET scan. (NCI) * detection of gamma rays emitted from tissues after administration of a natural substance such as glucose or fatty acids into which positron emitting isotopes have been incorporated; the paths of the gamma rays, which result from collisions of positrons and electrons, are interpreted by a computer algorithm, and the resultant tomogram represents local concentrations of the isotope containing substance. (CSP)
subclass of: Cross-sectional nuclear imaging protocol
disjoint with: SPECT imaging protocol
created date: 2007-03-07
modified date: 2007-03-07
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
has definition source: UMLS defSource
nif ID: _7_2.3
temp definition: An imaging protocol where images are acquired using a Positron Emission Tomography device.
umls cui: C0032743

Behavioral laterality
type: Class
subclass of: Behavioral phenotype
created date: 2006-04-04
modified date: 2006-10-11
externally sourced definition: A behavioral manifestation of cerebral dominance in which there is preferential use and superior functioning of either the left or the right side, as in the preferred use of the right hand or right foot. (MeSH)
has birnlex curator: Jeff Grethe
has curation status: pending final vetting
has external source: UMLS
umls cui: C0023114
scope note: This concept ID maps to the term "handedness" and "laterality" in the UMLS. We distinguish in BIRNLex between use of dominant hand (handedness) and other forms of behavioral laterality.

Anti saccade paradigm
type: Class
synonym: Anti-saccades paradigm
subclass of: Eye Saccade paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A behavioral paradigm in which subjects fixate a target and are instructed to make a saccade in the opposite direction of a stimulus (modified from Brain Map by OTF)
bonfire ID: BF_T0000341
has birnlex curator: Angie Laird
has birnlex curator: BIRN OTF
has birnlex curator: Jessica Turner
has curation status: uncurated
has external source: BrainMap.org

Algorithm execution
type: Class
subclass of: birnlex_11024
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A transformation that applies an algorithm with specified parameters on a data set on a specific computing platform.
has birnlex curator: Jeff Grethe
has curation status: curation complete

Temporal characteristic value
type: Class
subclass of: birnlex_11004
created date: 2007-03-07
modified date: 2007-03-07
has birnlex curator: BIRN OTF
has curation status: uncurated
temp definition: a type of quantitative value measured in units of time.

Oddball discrimination paradigm
type: Class
subclass of: Behavioral paradigm
disjoint with: Mismatch negativity paradigm
disjoint with: Deductive reasoning paradigm
disjoint with: Eye Saccade paradigm
disjoint with: Reading paradigm
disjoint with: Eating paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A behavioral paradigm that assesses a response to non-attended stimuli which are dissimilar to the majority of stimuli presented
bonfire ID: BF_T0000267
has birnlex curator: Jessica Turner
has curation status: curation complete

MRI protocol
type: Class
synonym: MRI
definition: * MRI uses radiofrequency waves and a strong magnetic field rather than x-rays to provide amazingly clear and detailed pictures of internal organs and tissues. The technique is valuable for the diagnosis of many pathologic conditions, including cancer, heart and vascular disease, stroke, and joint and musculoskeletal disorders. (NCI) * Non-invasive method of demonstrating internal anatomy based on the principle that atomic nuclei in a strong magnetic field absorb pulses of radiofrequency energy and emit them as radiowaves which can be reconstructed into computerized images. The concept includes proton spin tomographic techniques. (MSH) * non-invasive method of demonstrating internal anatomy based on the principle that atomic nuclei in a strong magnetic field absorb pulses of radiofrequency energy and emit them as radiowaves which can be reconstructed into computerized images; concept includes proton spin tomographic techniques. (CSP)
subclass of: Radiographic imaging protocol
disjoint with: Computer Axial Tomography imaging protocol
disjoint with: Ultrasonographic imaging protocol
disjoint with: Nuclear medicine imaging protocol
created date: 2007-03-07
modified date: 2008-05-01
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
has definition source: UMLS defSource
nif ID: _7_2.2
temp definition: An imaging protocol where images are acquired using a Magnetic Resonance Imaging device.
umls cui: C0024485

Handedness
type: Class
subclass of: Behavioral laterality
created date: 2006-04-04
modified date: 2006-10-11
birnlex definition: A behavioral attribute defined by the unequal distribution of fine motor skill between the left and right hands. Individuals more skilled with the right hand are called 'right-handed', and those more skilled with the left are 'left-handed'. A few people are equally skilled with both, and are termed 'ambidextrous'. (adapted from Wikipedia)
bonfire ID: BF_T0000316
has birnlex curator: Maryann Martone
has curation status: pending final vetting
has external source: UMLS

Covert visual reading paradigm
type: Class
subclass of: Reading paradigm
disjoint with: Covert braille reading paradigm
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Specimen preparation
type: Class
subclass of: birnlex_11022
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Mismatch negativity paradigm
type: Class
subclass of: Behavioral paradigm
disjoint with: Deductive reasoning paradigm
disjoint with: Eye Saccade paradigm
disjoint with: Reading paradigm
disjoint with: Eating paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: behavioral paradigm that assesses a response to non-attended stimuli which are dissimilar to the majority of stimuli presented.
bonfire ID: BF_T0000265
has birnlex curator: Jessica Turner
has curation status: uncurated

Intermediate voltage electron microscope
type: Class
subclass of: Transmission electron microscope
created date: 2006-05-15
modified date: 2006-10-11
birnlex definition: Transmission electron microscope cabable of operating at an accelerating voltage in the range of 300-400 KeV
bonfire ID: BF_T0000030
has birnlex curator: Maryann Martone
has curation status: uncurated

Longitudinal magnetization
type: Class
subclass of: Vector
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: The component (MZ) of the net magnetization vector in the direction of the static magnetic field. After RF excitation, this vector returns to its equilibrium value at a rate characterized by the time constant T1

Right handedness
type: Class
subclass of: Handedness
created date: 2006-04-04
modified date: 2006-10-11
birnlex definition: A behavioral phenotype where the subject preferentially uses the right hand for tasks requiring the use of a single hand or a dominant hand.
has birnlex curator: Maryann Martone
has curation status: uncurated
has external source: UMLS
umls cui: C0234417

Covert braille reading paradigm
type: Class
subclass of: Reading paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A behavioral paradigm in which a subject reads aloud with fingers.
bonfire ID: BF_T0000341
has birnlex curator: Angie Laird
has birnlex curator: Jessica Turner
has curation status: pending final vetting
has external source: BrainMap.org
scope note: Brain Map lists only a Braille reading paradigm but BIRNLex is dividing this into overt and covert Braille reading paradigms

Image reconstruction software
type: Class
subclass of: Image analysis software
subclass of: Restriction
  on property: RO_0000053
  some values from: Image reconstruction algorithm
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

High voltage electron microscope
type: Class
subclass of: Transmission electron microscope
created date: 2006-05-15
modified date: 2006-10-11
birnlex definition: transmission electron microscope cabable of operating an accelerating voltage in the range of 500- 1000 KeV
bonfire ID: BF_T0000029
has birnlex curator: BIRN OTF
has curation status: uncurated

Deductive reasoning paradigm
type: Class
subclass of: Behavioral paradigm
disjoint with: Eye Saccade paradigm
disjoint with: Reading paradigm
disjoint with: Eating paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A behavioral paradigm in which subjects are required to utilize problem-solving skills and logic to determine the correct solution; feedback is sometimes given.
bonfire ID: BF_T0000345
has birnlex curator: Angie Laird
has birnlex curator: Jessica Turner
has curation status: uncurated
has external source: BrainMap.org

Longitudinal relaxation time
type: Class
subclass of: Relaxation time
editorial note: We may want to eventually include the 1/e mathematical definition of relaxation time.
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: BIRN OTF
has curation status: uncurated
temp definition: a type of temporal characteristic value where the time meansured is the time requird for the longitudinal magnetization to return to its equilibrium value after excitation due to the exchange of energy between the nuclear spins and the lattice.

Software toolkit
type: Class
subclass of: Digital aggregate entity
created date: 2007-03-07
modified date: 2007-03-07
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: Software delivered in source or binary form as a collection of independent modules whereby the kit components can be used independently of each other or included as part of another program (derived from NCBC Software Ontology) (BB:2007-03-07).

Image processing software
type: Class
definition: An application or program that is used for any form of signal processing for which the input is an image, such as photographs, magnetic resonance images, or frames of video; the output of image processing can be either an image or a set of characteristics or parameters related to the image.
subclass of: Data processing software
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Ultrahigh voltage electron microscope
type: Class
abbrev: UHVEM
subclass of: Transmission electron microscope
created date: 2006-05-15
modified date: March 31, 2009
birnlex definition: Transmission electron microscope capable of operating at an accelerating voltage of > 1 MeV
bonfire ID: BF_T0000031
has birnlex curator: BIRN OTF
has curation status: uncurated

T2 weighted protocol
type: Class
synonym: T2 weighted scan
definition: An MRI scanning pulse sequence that is used to acquire structural data whose tissue contrast parameter is T2-weighted.
subclass of: Anatomical MRI protocol
created date: 2007-03-07
modified date: February 5, 2009
has birnlex curator: BIRN OTF
has curation status: uncurated
temp definition: An imaging protocol typically using longer TE and TR times whose contrast and brightness are predominately determined by T2 signals (2007-03-07)

Eye Saccade paradigm
type: Class
subclass of: Behavioral paradigm
disjoint with: Reading paradigm
disjoint with: Eating paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A behavioral paradigm in which a subject makes a rapid eye movement relative to an initial target (JB).
bonfire ID: BF_T0000360
has birnlex curator: Jyl Boline
has curation status: pending final vetting
has external source: BrainMap.org
scope note: BIRN uses this term to refer to any paradigm involving a saccadic eye movement. These paradigms include both saccdic movements to and away from the target. Note that this usage differs from that in Brain Map.

Image analysis software
type: Class
subclass of: Data processing software
change note: Moved as a subclass of Data processing software from Data analysis software.
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated
has former parent class: Data analysis software

Electron tomography software
type: Class
subclass of: Image reconstruction software
created date: 2006-05-15
modified date: 2006-10-11
has birnlex curator: Maryann Martone
has curation status: uncurated

Diffusion tensor imaging protocol
type: Class
synonym: DTI
definition: A magnetic resonance imaging protocol that is sensitive to the diffusion of water molecules and measures this diffusion in 6 or greater directions. (February 9, 2009)
subclass of: Diffusion-weighted imaging protocol
change note: Moved as a subclass of 'Diffusion-weighted imaging protocol' from 'Structural MRI protocol'.
created date: 2007-03-07
modified date: 2007-03-07
modified date: February 9, 2009
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
has former parent class: birnlex_2251
temp definition: Diffusion Tensor Imaging: an imaging technique that enables the measurement of the restricted diffusion of water in tissue. The principal application is in the imaging of white matter where the location, orientation, and anisotropy of the tracts can be measured. The architecture of the axons in parallel bundles, and their myelin sheaths, facilitate the diffusion of the water molecules preferentially along their main direction. Such preferentially oriented diffusion is called anisotropic diffusion. If we apply diffusion gradients (i.e. magnetic field variations in the MRI magnet) in at least 6 directions, it is possible to calculate, for each voxel, a tensor (i.e. a symmetric positive definite 3by3 matrix) that describes the 3-dimensional shape of diffusion. The fiber direction is indicated by the tensor's main eigenvector. (from Wikipedia).

Reading paradigm
type: Class
subclass of: Behavioral paradigm
disjoint with: Eating paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: A behavioral paradigm in which a subject is asked to read either silently (covert) or aloud (overt)
bonfire ID: BF_T0000361
has birnlex curator: BIRN OTF
has curation status: pending final vetting
pending action note: This list contains precoordinated terms that will be addressed at a future date.
scope note: This term does not differentiate between lexical and semantic parsing by the subject

Co-investigator
type: Class
subclass of: birnlex_11015
created date: 2006-07-15
modified date: 2007-03-05
has birnlex curator: Maryann Martone
has curation status: uncurated

Imaging platform
type: Class
subclass of: birnlex_11030
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Control group
type: Class
deprecated: true
subclass of: DeprecatedClass
created date: 2006-06-01
modified date: 2007-03-05
externally sourced definition: Subject group that serves as a standard for comparison in experimental studies. It is similar in relevant characteristics to the experimental group but do not receive the experimental intervention. (MeSH)
has birnlex curator: Maryann Martone
has curation status: uncurated
has external source: UMLS
has former parent class: OBI 176
is replaced by class: birnlex_11044
umls cui: C0009932

Image reconstruction algorithm
type: Class
subclass of: birnlex_11009
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: Algorithm used to compute a reconstruction from a set of images, e.g., R-weighted back projection.
bonfire ID: BF_T0000131
has birnlex curator: Maryann Martone
has curation status: curation complete

Eating paradigm
type: Class
subclass of: Behavioral paradigm
created date: 2006-06-01
modified date: 2006-10-11
birnlex definition: Behavioral paradigm in which the subject ingests food.
bonfire ID: BF_T0000357
has birnlex curator: Angie Laird
has birnlex curator: Jessica Turner
has curation status: uncurated
has external source: BrainMap.org

Magnetic resonance imaging platform
type: Class
subclass of: Imaging platform
created date: 2006-06-01
modified date: 2006-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Echo planar imaging protocol
type: Class
synonym: EPI
subclass of: Functional MRI protocol
created date: 2007-03-07
modified date: 2007-03-07
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: Echo Planar Imaging: the utilization of rapid gradient reversal pulses of the readout gradient resulting in a series of gradient echo signals to reduce fast dephasing or signal loss. This is the primary imaging method for fMRI.

Transverse magnetization
type: Class
subclass of: Vector
created date: 2007-03-09
modified date: 2007-03-09
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: The component of the net magnetization vector at right angles to the main magnetic field. Precession of the transverse magnetization at the Larmor frequency is responsible for the detectable NMR signal. In the absence of externally applied RF energy, the transverse magnetization will decay to zero with a characteristic time constant of T2, or more strictly T2*.

Relational database
type: Class
deprecated: true
subclass of: DeprecatedClass
comment: I think this class should be retired and we should just go with at the level of resource descriptors. Does a user really care what the underlying technology or data model is? (Maryann Martone)
created date: 2007-10-09
modified date: March 31, 2009
has birnlex curator: Bill Bug
has curation status: uncurated
has former parent class: birnlex_11006
nif ID: _1_1.1
temp definition: A normalized data set constructed according to a specific entity-relation data model.

Data acquisition software
type: Class
definition: A resource that provides software that assists in measuring, recording, and collecting information about a physical phenomenon or physical property of an object (under investigation). Examples include the temperature or temperature change of a room, the reaction time of a response, digital picture acquisition.
subclass of: Data processing software
version info: 90413
created date: 2007-10-09
modified date: June 12, 2011
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _1_2.1

Documentation generation software
type: Class
definition: A resource that provides a programming tool that generates documentation intended for programmers (API documentation) or end users (End-user Guide), or both, from a set of specially commented source code files, and in some cases, binary files.
subclass of: Software development tool
created date: 2007-10-09
modified date: June 11, 2011
has birnlex curator: Bill Bug
has curation status: uncurated

Data processing software
type: Class
synonym: Data operations software
subclass of: birnlex_11012
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _1_2.2

Data analysis software
type: Class
definition: A resource that provides an application or program that is used to gather, model, and transform data with the goal of highlighting useful information, suggesting conclusions, and supporting decision making.
subclass of: Data processing software
created date: 2007-10-09
modified date: June 12, 2011
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _4_14

Image acquisition software
type: Class
subclass of: Data acquisition software
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated

Data visualization software
type: Class
definition: A resource that provides an application or program that is used for the study of the visual representation of data, defined as information which has been abstracted in some schematic form, including attributes or variables for the units of information.
subclass of: Data processing software
created date: 2007-10-09
modified date: September 10, 2009
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _1_2.3
nif ID: _7_18

Sequence analysis software
type: Class
synonym: 1D correlative analysis software
synonym: sequence pattern analysis software
subclass of: Data analysis software
subclass of: Restriction
  on property: RO_0000053
  some values from: Sequence-based model
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: BIRN OTF
has curation status: uncurated
nif ID: _1_2.2.3

Time-series analysis software
type: Class
subclass of: Data analysis software
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: BIRN OTF
has curation status: uncurated

1D Time-series analysis software
type: Class
subclass of: Time-series analysis software
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: BIRN OTF
has curation status: uncurated
nif ID: _1_2.2.2

2D Time-series analysis software
type: Class
subclass of: Time-series analysis software
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: BIRN OTF
has curation status: uncurated

3D Time-series analysis software
type: Class
synonym: 4D analysis software
subclass of: Time-series analysis software
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: BIRN OTF
has curation status: uncurated

Network analysis software
type: Class
synonym: pathway analysis software
subclass of: Data analysis software
subclass of: Restriction
  on property: RO_0000053
  some values from: Network interaction model
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: BIRN OTF
has curation status: uncurated
nif ID: _1_2.2.4

3D visualization software
type: Class
subclass of: Data visualization software
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _1_2.3.1

4D visualization software
type: Class
subclass of: Data visualization software
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _1_2.3.1

Software development tool
type: Class
subclass of: birnlex_11012
created date: 2007-03-07
modified date: 2007-03-07
has birnlex curator: Bill Bug
has curation status: uncurated

Data compression software
type: Class
subclass of: Data processing software
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated

Software development environment
type: Class
synonym: Integrated Software development environment
definition: A resource that provides the entire environment (applications, servers, network) that provides comprehensive facilities to computer programmers for software development. An SDE typically includes an integrated development environment (IDE, comprising source code editor, compiler, build automation, debugger), requirement management tools, design modeling tools, documentation generation tools, code analysis tools, and so on.
subclass of: Software development tool
version info: 145595
created date: 2007-03-07
modified date: June 11, 2011
acronym: IDE
has birnlex curator: Bill Bug
has curation status: uncurated

Compiler
type: Class
definition: A resource that provides a computer program (or set of programs) that transforms source code written in a computer language (the source language) into another computer language (the target language, often having a binary form known as object code). The most common reason for wanting to transform source code is to create an executable program. A \\u201ccompiler\\u201d is primarily used for programs that translate source code from a high-level programming language to a lower level language (e.g., assembly language or machine language), and is likely to perform many or all of the following operations: lexical analysis, preprocessing, parsing, semantic analysis, code generation, and code optimization.
subclass of: Software development tool
created date: 2007-03-07
modified date: June 11, 2011
has birnlex curator: Bill Bug
has curation status: uncurated

Code Profiler
type: Class
alternative label: Code profiler
definition: A resource that provides a performance analysis tool that measures the behavior of a program as it executes, particularly the frequency and duration of function calls. The profiling process helps to determine which subroutines (or just snippets of code) take longest to execute and which subroutines are called most often. Code profilers are used when you suspect that some part of your code is called very often and maybe there is a need to optimize it, which could significantly improve the overall performance. Profilers use a wide variety of techniques to collect data, including hardware interrupts, code instrumentation, instruction set simulation, operating system hooks, and performance counters.
subclass of: Software development tool
created date: 2007-03-07
modified date: June 11, 2011
has birnlex curator: Bill Bug
has curation status: uncurated

Code testing framework
type: Class
definition: A resource that provides a software environment created to investigate the quality of the product or service under test, with respect to the context in which it is intended to operate. This includes, but is not limited to, the process of executing a program or application with the intent of finding software bugs.
subclass of: Software development tool
created date: 2007-03-07
modified date: June 11, 2011
has birnlex curator: Bill Bug
has curation status: uncurated

Segmentation software
type: Class
definition: Software application for the generation of the 'Segmentation' of input data into regions of 'homogeneous' characteristic. Various characteristics can be utilized to influence the selection of regions as targets for the segmentation (NITRC).
subclass of: Image analysis software
created date: 2007-10-09
modified date: April 1, 2009
modified date: October 20, 2012
has external source: NITRC
nitrc ID: NITRC_333

Image alignment software
type: Class
deprecated: true
preferred label: Alignment software
synonym: Alignment software
synonym: image registration software
definition: Software application that performs image spatial transformation for the purposes of image 'Registration'. (NITRC)
subclass of: DeprecatedClass
comment: This class has been retired
change note: Added: synonyms, definition and new label. (April 2, 2009)
created date: 2007-10-09
modified date: April 2, 2009
modified date: April 24, 2009
has birnlex curator: Bill Bug
has curation status: uncurated
has former parent class: Image analysis software
is replaced by class: Registration software
nitrc ID: 388

Registration software
type: Class
synonym: Image Alignment software
subclass of: Image analysis software
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated

Data access protocol
type: Class
subclass of: birnlex_11010
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: BIRN OTF
has curation status: uncurated
nif ID: _2.2_6

Static HTML document
type: Class
subclass of: Data access protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: BIRN OTF
has curation status: uncurated
nif ID: _2.2_1

Dynamic HTML document
type: Class
subclass of: Data access protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: BIRN OTF
has curation status: uncurated
nif ID: _2.2_2

Web service
type: Class
definition: A resource that provides a software system designed to support interoperable machine-to-machine interaction over a network. Web services are frequently Web APIs that can be accessed over a network, such as the Internet, and executed on a remote system hosting the requested services.
subclass of: Data access protocol
version info: 90426
created date: 2007-10-09
modified date: 2007-10-09
modified date: June 15, 2011
has birnlex curator: BIRN OTF
has curation status: uncurated
nif ID: _2.2_4

Application programming interface
type: Class
subclass of: Data access protocol
created date: 2007-10-09
modified date: 2007-10-09
acronym: API
has birnlex curator: BIRN OTF
has curation status: uncurated

SPECT imaging protocol
type: Class
synonym: Single Photon Emission Computed Tomography imaging protocol
definition: * A method of computed tomography that uses radionuclides which emit a single photon of a given energy. The camera is rotated 180 or 360 degrees around the patient to capture images at multiple positions along the arc. The computer is then used to reconstruct the transaxial, sagittal, and coronal images from the 3-dimensional distribution of radionuclides in the organ. The advantages of SPECT are that it can be used to observe biochemical and physiological processes as well as size and volume of the organ. The disadvantage is that, unlike positron-emission tomography where the positron-electron annihilation results in the emission of 2 photons at 180 degrees from each other, SPECT requires physical collimation to line up the photons, which results in the loss of many available photons and hence degrades the image. (MSH) * method of computed tomography that uses radionuclides which emit a single photon of a given energy: the camera is rotated 180 or 360 degrees around the subject to capture images at multiple positions along the arc; the computer is then used to reconstruct the transaxial, sagittal, and coronal images from the three-dimensional distribution of radionuclides in the organ. (CSP)
subclass of: Cross-sectional nuclear imaging protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
has definition source: UMLS defSource
nif ID: _7_2.4
umls cui: C0040399

EM imaging protocol
type: Class
synonym: Electron microscopy imaging protocol
subclass of: Imaging protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_4

SEM imaging protocol
type: Class
synonym: Scanning electron microscopy imaging protocol
subclass of: EM imaging protocol
disjoint with: TEM imaging protocol
disjoint with: Electron Energy Loss Spectroscopy imaging protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_4.1

TEM imaging protocol
type: Class
synonym: Transmission electron microscopy imaging protocol
subclass of: EM imaging protocol
disjoint with: Electron Energy Loss Spectroscopy imaging protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_4.2

STEM imaging protocol
type: Class
synonym: Scanning transmission electron microscopy imaging protocol
subclass of: TEM imaging protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_4.3

Immunohistochemical protocol
type: Class
abbrev: IHC
definition: A protocol that specifies the process of immunohistochemistry. Immunohistochemistry is the process of localizing proteins in cells of a tissue section exploiting the principle of antibodies binding specifically to antigens in biological tissues. It takes its name from the roots "immuno," in reference to antibodies used in the procedure, and "histo," meaning tissue (compare to immunocytochemistry). (from wikipedia)
subclass of: Microscopy contrast enhancement protocol
editorial note: Note: Some use the term "immunohistochemistry" to refer to protocols that employ an enzymatic chromagen as opposed to a particulate or fluorescent marker. Going back to the original Greek (histo=tissue), we have chosen the current definition. (Maryann Martone)
created date: 2007-10-09
modified date: June 24, 2009
has birnlex curator: BIRN OTF
has curation status: uncurated
nif ID: _7_6.2.3

Fluorescence labeling protocol
type: Class
subclass of: Microscopy contrast enhancement protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: BIRN OTF
has curation status: uncurated

Golgi staining protocol
type: Class
subclass of: Staining protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: BIRN OTF
has curation status: uncurated
nif ID: _7_6.2.1

Immunocytochemistry protocol
type: Class
subclass of: Microscopy contrast enhancement protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: BIRN OTF
has curation status: uncurated
nif ID: _7_6.2.2

network graph visualization software
type: Class
subclass of: Data visualization software
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated

Version source control system
type: Class
synonym: (source) code management
synonym: Revision control
synonym: Source control
synonym: Version control (system)
definition: A resource that provides a system for the management of multiple revisions of the same unit of information. It is most commonly used in engineering and software development to manage ongoing development of digital documents like application source code, art resources such as blueprints or electronic models, and other projects that may be worked on by a team of people.
subclass of: Software development tool
version info: 90411
created date: 2007-03-07
modified date: June 11, 2011
has birnlex curator: Bill Bug
has curation status: uncurated

Nissl staining protocol
type: Class
subclass of: Staining protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: BIRN OTF
has curation status: uncurated
nif ID: _7_6.2.6

Myelin staining protocol
type: Class
subclass of: Staining protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: BIRN OTF
has curation status: uncurated
nif ID: _7_6.2.4

Radiolabeling protocol
type: Class
subclass of: Microscopy contrast enhancement protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: BIRN OTF
has curation status: uncurated
nif ID: _7_6.4

Functional MRI protocol
type: Class
synonym: fMRI
subclass of: MRI protocol
disjoint with: Structural MRI protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_2.2.2

Structural MRI protocol
type: Class
synonym: MRI
definition: A structural MRI protocol is an MRI protocol that provides information to qualitatively and quantitatively describe the shape, size, and integrity of gray and white matter structures in the brain.
subclass of: MRI protocol
created date: 2007-10-09
modified date: 2007-10-09
defining citation URI: http://fmri.ucsd.edu/Research/whatisfmri.html
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_2.2.1

Optical imaging protocol
type: Class
synonym: Light microscopy imaging protocol
subclass of: Imaging protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_7

Light transmission optical imaging protocol
type: Class
subclass of: Optical imaging protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated

Light emitting optical imaging protocol
type: Class
synonym: fluorescence/chemiluminescence/phosphorescence optical imaging protocol
subclass of: Optical imaging protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_7.3

Bright-field imaging protocol
type: Class
subclass of: Light transmission optical imaging protocol
disjoint with: Dark-field imaging protocol
disjoint with: Differential interference contrast imaging protocol
disjoint with: Phase contrast imaging protocol
disjoint with: Polarization contrast imaging protocol
disjoint with: Total internal reflection imaging protocol
created date: 2007-10-09
modified date: 2008-05-01
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_7.1

Dark-field imaging protocol
type: Class
subclass of: Light transmission optical imaging protocol
disjoint with: Differential interference contrast imaging protocol
disjoint with: Phase contrast imaging protocol
disjoint with: Polarization contrast imaging protocol
disjoint with: Total internal reflection imaging protocol
created date: 2007-10-09
modified date: 2008-05-01
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_7.2

Multiphoton imaging protocol
type: Class
synonym: Multiphoton imaging
synonym: Multiphoton microscopy
definition: An imaging protocol that produces images using a microscopy in multiphoton mode.
subclass of: Light emitting optical imaging protocol
disjoint with: Confocal imaging protocol
disjoint with: Fluorescence resonance energy transfer imaging protocol
disjoint with: Spectroscopic imaging protocol
disjoint with: Wide-field fluorescence imaging protocol
change note: Added: definition and synonyms (April 2, 2009)
created date: 2007-10-09
modified date: April 2, 2009
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_7.3.1

Confocal imaging protocol
type: Class
synonym: confocal imaging
synonym: confocal microscopy
subclass of: Light emitting optical imaging protocol
disjoint with: Fluorescence resonance energy transfer imaging protocol
disjoint with: Spectroscopic imaging protocol
disjoint with: Wide-field fluorescence imaging protocol
change note: Synonyms added (April 2, 2009)
created date: 2007-10-09
modified date: April 2, 2009
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_7.3.2

Laser scanning confocal imaging protocol
type: Class
subclass of: Confocal imaging protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated

Fluorescence resonance energy transfer imaging protocol
type: Class
synonym: FRET protocol
subclass of: Light emitting optical imaging protocol
disjoint with: Spectroscopic imaging protocol
disjoint with: Wide-field fluorescence imaging protocol
created date: 2007-10-09
modified date: June 23, 2009
acronym: FRET
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_7.3.3

Differential interference contrast imaging protocol
type: Class
synonym: Differential interference contrast microscopy
synonym: Nomarski optical imaging protocol
subclass of: Light transmission optical imaging protocol
disjoint with: Phase contrast imaging protocol
disjoint with: Polarization contrast imaging protocol
disjoint with: Total internal reflection imaging protocol
created date: 2007-10-09
modified date: 2008-05-01
acronym: DIC
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_7.4

Phase contrast imaging protocol
type: Class
synonym: Phase contrast microscopy
subclass of: Light transmission optical imaging protocol
disjoint with: Polarization contrast imaging protocol
disjoint with: Total internal reflection imaging protocol
created date: 2007-10-09
modified date: 2008-05-01
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_7.5

Polarization contrast imaging protocol
type: Class
synonym: Polarization microscopy
subclass of: Light transmission optical imaging protocol
disjoint with: Total internal reflection imaging protocol
created date: 2007-10-09
modified date: 2008-05-01
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_7.6

Total internal reflection imaging protocol
type: Class
synonym: Total internal reflection microscopy
subclass of: Light transmission optical imaging protocol
created date: 2007-10-09
modified date: 2008-05-01
acronym: TIRM
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_7.7

Intrinsic emission imaging protocol
type: Class
synonym: Intrinsic emission microscopy
subclass of: Multiphoton imaging protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_7.8

Spectroscopic imaging protocol
type: Class
synonym: Spectroscopic microscopy
subclass of: Light emitting optical imaging protocol
disjoint with: Wide-field fluorescence imaging protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_7.9

Electron Energy Loss Spectroscopy imaging protocol
type: Class
synonym: Electron Energy Loss Spectroscopy
subclass of: EM imaging protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated

Computer Axial Tomography imaging protocol
type: Class
synonym: CAT imaging protocol
synonym: CT Imaging protocol
subclass of: Radiographic imaging protocol
disjoint with: Ultrasonographic imaging protocol
disjoint with: Nuclear medicine imaging protocol
created date: 2007-10-09
modified date: 2007-10-09
acronym: CAT
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_2.1

Electrical recording protocol
type: Class
synonym: Electrophysiology
subclass of: birnlex_11010
created date: 2007-10-09
modified date: 2007-10-09
modified date: April 8, 2010
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_3

Micro-electrode recording protocol
type: Class
subclass of: Electrical recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated

Macro-electrode recording protocol
type: Class
subclass of: Electrical recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_3.4

Extracellular electrode recording protocol
type: Class
subclass of: Micro-electrode recording protocol
disjoint with: Intracellular electrode recording protocol
disjoint with: Ion channel recording protocol
disjoint with: Amperometric electrode recording protocol
disjoint with: Electromyography surface recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_3.1

Intracellular electrode recording protocol
type: Class
subclass of: Micro-electrode recording protocol
disjoint with: Ion channel recording protocol
disjoint with: Amperometric electrode recording protocol
disjoint with: Electromyography surface recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_3.2

Ion channel recording protocol
type: Class
subclass of: Micro-electrode recording protocol
disjoint with: Amperometric electrode recording protocol
disjoint with: Electromyography surface recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_3.2.2

Amperometric electrode recording protocol
type: Class
subclass of: Micro-electrode recording protocol
disjoint with: Electromyography surface recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_3.3

Single electrode extracellular recording protocol
type: Class
subclass of: Extracellular electrode recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_3.1.1

Grid electrode recording protocol
type: Class
subclass of: Electrical recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_3.4

Current clamp voltage recording protocol
type: Class
subclass of: Intracellular electrode recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated

Voltage clamp current recording protocol
type: Class
subclass of: Intracellular electrode recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_3.2.1

Single-electrode voltage clamp recording protocol
type: Class
subclass of: Voltage clamp current recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated

Whole-cell voltage clamp recording protocol
type: Class
subclass of: Single-electrode voltage clamp recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated

Multiple-electrode voltage clamp recording protocol
type: Class
subclass of: Voltage clamp current recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated

Cell-attached single-channel recording protocol
type: Class
subclass of: Ion channel recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated

Cell-detached single-channel recording protocol
type: Class
subclass of: Ion channel recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated

Cell-detached inside-out single-channel recording protocol
type: Class
subclass of: Cell-detached single-channel recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated

Cell-detached inside-out single-channel recording protocol
type: Class
preferred label: Cell-detached outside-out single-channel recording protocol
subclass of: Cell-detached single-channel recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated

Reconstituted bilayer single-channel patch recording protocol
type: Class
subclass of: Ion channel recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated

Reconstituted bilayer electrical recording protocol
type: Class
subclass of: Electrical recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated

Ion-sensitive electrode recording protocol
type: Class
subclass of: Amperometric electrode recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_3.3.2

pH-sensitive electrode recording protocol
type: Class
subclass of: Ion-sensitive electrode recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_3.3.1

Cuff-electrode recording protocol
type: Class
synonym: Suction electrode recording protocol
subclass of: Macro-electrode recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_3.4.1

Field electrode recording protocol
type: Class
synonym: Surface electrode recording protocol
subclass of: Macro-electrode recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_3.4.2

Electroencephalography recording protocol
type: Class
subclass of: Field electrode recording protocol
created date: 2007-10-09
modified date: 2007-10-09
acronym: EEG
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_3.4.2

Electrocardiography recording protocol
type: Class
subclass of: Field electrode recording protocol
created date: 2007-10-09
modified date: 2007-10-09
acronym: ECG
acronym: EKG
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_3.4.2_7_11.1

In-situ hybridization protocol
type: Class
subclass of: Specimen preparation protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_5.2

Indentifying value
type: Class
subclass of: birnlex_11003
created date: 2007-10-05
modified date: 2007-10-05
has birnlex curator: Bill Bug
has curation status: graph position temporary

Accession number
type: Class
synonym: Accession
subclass of: Indentifying value
created date: 2007-10-05
modified date: 2007-10-05
has birnlex curator: Bill Bug
has curation status: graph position temporary

Primary key
type: Class
subclass of: Indentifying value
created date: 2007-10-05
modified date: 2007-10-05
has birnlex curator: Bill Bug
has curation status: graph position temporary

Life Science Indenfier
type: Class
subclass of: Indentifying value
created date: 2007-10-05
modified date: 2007-10-05
acronym: LSID
has birnlex curator: Bill Bug
has curation status: graph position temporary

Computational model
type: Class
subclass of: birnlex_11009
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _4_9
temp definition: A mathematical description of a inter-connected and/or dynamic biological system.

Nerve cell model
type: Class
deprecated: true
synonym: Computational neuronal model
subclass of: DeprecatedClass
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated
has former parent class: Computational model
is replaced by class: Nerve cell structural model
is replaced by class: Nerve cell functional model
temp definition: A mathematical description of the structure or function of nerve cells and/or their cellular compartments.

Nerve cell structural model
type: Class
synonym: neuronal structure model
subclass of: Structural model
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: A mathematical description of the structure of nerve cells and/or their cellular compartments.

Nerve cell functional model
type: Class
synonym: computational neuronal model
synonym: neuronal physiological model
subclass of: Physiological model
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: A mathematical description of the physiological funcion of nerve cells and/or their cellular compartments.

Ionic current model
type: Class
synonym: Membrane current model
subclass of: Physiological model
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: A mathematical description of the temporal and voltage dependencies of particular, ion-selective membrane currents.

Protein folding model
type: Class
subclass of: Structural model
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated

Network interaction model
type: Class
subclass of: Computational model
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated

Pathway model
type: Class
synonym: enzyme network model
synonym: regulatory network model
synonym: signaling pathway model
subclass of: Network interaction model
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated

Gene regulatory network model
type: Class
synonym: Gene network model
subclass of: Network interaction model
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated

Physiological model
type: Class
synonym: Physiological system model
definition: A mathematical description of the complex physical and temporal dependencies between a set of related biological entities and their immediated environment.
subclass of: Computational model
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated

Structural model
type: Class
definition: A coordinate-based mathematical description of a collection of biological structures.
subclass of: Computational model
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated

Macroscopic anatomical structure model
type: Class
synonym: anatomical model
subclass of: Structural model
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: A mathematical description of the structure of organs and organ regions.
example: Finite element decomposition of anatomical structure
example: Mesh model of brain structure
example: Wavelet-based multi-resolution decomposition of anatomical structure

Multi-cell model
type: Class
synonym: tissue model
subclass of: Physiological model
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: A mathematical description of the temporal dependencies of a related set of biological cells

Neural circuit model
type: Class
synonym: circuit model
synonym: nerve cell circuit model
synonym: neural network model
subclass of: Multi-cell model
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: A mathematical description of the temporal activity dependence of a related set of neuronal cells typically composed of nerve cell models, specific intercellular transmission relations (neurochemical and electrotonic), and enviormental influences.

Body system model
type: Class
subclass of: Physiological model
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: A mathematical description of the temporal activity dependence of an extended set of tissues and cells across an entire organism.

Sequence-based model
type: Class
definition: A mathematical description of the relatedness of a set of nucleic acid or amino acid sequences based on a correlative comparison of the sequences or properties derived from those sequences.
subclass of: Computational model
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated

Sequence homology model
type: Class
synonym: homology model
definition: A mathematical description of the phylogenetic relatedness of a set of nucleic acid sequences based on a correlative comparison of linear sequence.
subclass of: Sequence-based model
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated

Hydrophobicity model
type: Class
synonym: hydrophobicity analysis
synonym: hydrophobicity plot
definition: A mathematical description of the solvent interaction properties of an amino acid sequence based on the biophysical properties of the amino acid side chain moeties. Such models are used to indicate putative internal hydrophobic domains and transmembrane spanning regions in polypeptides.
subclass of: Sequence-based model
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated

Protein structure classification
type: Class
synonym: protein classification
definition: A mathematical description of the related structural domains of a collection of amino acid sequence based on the consensus sequences with defined structural properties (e.g., alpha helix, beta sheet, etc.). These models are typically used to infer phylogenetic relatedness of proteins (families/superfamilies) based on structural properties.
subclass of: Sequence-based model
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated

Signal processing software
type: Class
subclass of: Data processing software
subclass of: Restriction
  on property: RO_0000053
  some values from: Signal processing algorithm
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_17

Signal processing algorithm
type: Class
synonym: Digital signal processing algorithm
synonym: DSP algorithm
definition: A mathematical separation and/or combination of time-series data typically performed in real-time and utilizing Fourier transform methods to manipulate the distinct frequency components of a set of an input data stream to produce an output data stream.
subclass of: birnlex_11009
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated

Pipeline processing software
type: Class
synonym: workflow processing software
subclass of: Systems interoperability software
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Graphical pipeline construction software
type: Class
subclass of: Pipeline processing software
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Systems interoperability software
type: Class
definition: A resource that provides an application or program with the capability to exchange data with different programs via a common set of exchange formats, to read and write the same file formats, and to use the same protocols. According to ISO/IEC 2382-01, Information Technology Vocabulary, Fundamental Terms, interoperability is "the capability to communicate, execute programs, or transfer data among various functional units in a manner that requires the user to have little or no knowledge of the unique characteristics of those units".
subclass of: birnlex_11012
version info: 146952
created date: 2007-10-11
modified date: June 11, 2011
has birnlex curator: BIRN OTF
has curation status: uncurated

GRID computing software
type: Class
subclass of: Systems interoperability software
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Portlet component
type: Class
subclass of: Systems interoperability software
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Subject report
type: Class
subclass of: birnlex_11042
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _7_12.2

Human subject report
type: Class
synonym: patient report
subclass of: Subject report
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary

Literature corpus
type: Class
synonym: literature
subclass of: birnlex_11001
created date: 2007-10-09
modified date: February 12, 2010
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _1_4
nif ID: _4_6.4
temp definition: A collection of unstructured, scientific literature.

Lexical processing algorithm
type: Class
synonym: Text-mining algorithm
definition: Any text-based algorithm used to match strings against a controlled lexicon and/or infer syntactic structure or semantic conent from a corpus of unstructured text.
subclass of: birnlex_11009
created date: 2007-10-10
modified date: 2007-10-10
has birnlex curator: Bill Bug
has curation status: uncurated

Natural language processing algorithm
type: Class
definition: Natural language processing (NLP) is a subfield of artificial intelligence and linguistics. It studies the problems of automated generation and understanding of natural human languages. Natural language generation systems convert information from computer databases into normal-sounding human language, and natural language understanding systems convert samples of human language into more formal representations that are easier for computer programs to manipulate.
subclass of: Lexical processing algorithm
created date: 2007-10-11
modified date: 2007-10-11
acronym: NLP
has birnlex curator: Bill Bug
has curation status: uncurated
has definition source: Wikipedia defSource

Part-of-speech tagging algorithm
type: Class
definition: Part-of-speech tagging (POS tagging or POST), also called grammatical tagging, is the process of marking up the words in a text as corresponding to a particular part of speech, based on both its definition, as well as its context, i.e., relationship with adjacent and related words in a phrase, sentence, or paragraph. A simplified form of this is commonly taught school-age children, in the identification of words as nouns, verbs, adjectives, adverbs, etc. Once performed by hand, POS tagging is now done in the context of computational linguistics, using algorithms which associate discrete terms, as well as hidden parts of speech, in accordance with a set of descriptive tags.
subclass of: Natural language processing algorithm
created date: 2007-10-11
modified date: 2007-10-11
acronym: POST
has birnlex curator: Bill Bug
has curation status: uncurated
has definition source: Wikipedia defSource
example: Baum-Welch algorithm
example: Brill Tagger
example: Viterbi algorithm

Bibliographic database
type: Class
deprecated: true
subclass of: DeprecatedClass
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
has former parent class: birnlex_11006
nif ID: _1_4
temp definition: A collection bibliographic records describing published works from the scientific literature which may or may not contain abstracts

Structured knowledge resource
type: Class
synonym: Structured data resource
subclass of: birnlex_11001
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _1_4
nif ID: _4_8
temp definition: A collection data records arranged according to some semantic framework. The semantic framework may be minimally expressive - such as a simple controlled vocabulary - of highly expressive such as a formally structured ontology. Such resources may include only a representation of universal/classes/categories or may be linked to individual instance data typed according to a set of asserted classes (i.e., a knowledgebase).

Controlled vocabulary
type: Class
synonym: controllled terminology
synonym: terminology
definition: In library and information science controlled vocabulary is a carefully selected list of words and phrases, which are used to tag units of information (document or work) so that they may be more easily retrieved by a search. Controlled vocabularies solve the problems of homographs, synonyms and polysemes by ensuring that each concept is described using only one authorized term and each authorised term in the controlled vocabulary describes only one concept. In short, controlled vocabularies reduce ambiguity inherent in normal human languages where the same concept can be given different names and ensure consistency. Controlled vocabulary schemes mandate the uses of predefined, authorised terms that have been preselected by the designer of the controlled vocabulary as opposed to natural language vocabularies where there is no restriction on the vocabulary that can be used.
subclass of: Structured knowledge resource
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has definition source: Wikipedia defSource
nif ID: _2.4
nif ID: _4_8.2
example: Medical Subject Headings (MeSH)
example: Systematized Nomenclature of Medicine (SNOMED)

Classification scheme
type: Class
definition: Structured grouping of entities based on a correspondence of derived physicochemical properties.
subclass of: Structured knowledge resource
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
example: PFAM
example: Structural Classification of Proteins (SCOP)

Taxonomy
type: Class
definition: A taxonomy, or taxonomic scheme, is composed of taxonomic units known as taxa (singular taxon), or kinds of things that are arranged frequently in a hierarchical structure, typically related by subtype-supertype relationships, also called parent-child relationships. In such a subtype-supertype relationship the subtype kind of thing has by definition the same constraints as the supertype kind of thing plus one or more additional constraints. For example, car is a subtype of vehicle. So any car is also a vehicle, but not every vehicle is a car. So, a thing needs to satisfy more constraints to be a car than to be a vehicle.
subclass of: Structured knowledge resource
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has definition source: Wikipedia defSource

Thesaurus
type: Class
definition: A formal definition of a thesaurus designed for indexing is: * a list of every important term (single-word or multi-word) in a given domain of knowledge; and * a set of related terms for each term in the list. Terms are the basic semantic units for conveying concepts. They are usually single-word nouns, since nouns are the most concrete part of speech. Verbs can be converted to nouns -- cleans to cleaning, reads to reading, and so on. Adjectives and adverbs, however, seldom convey any meaning useful for indexing. When a term is ambiguous, a "scope note" can be added to ensure consistency, and give direction on how to interpret the term. Naturally, not every term needs a scope note, but their presence is of considerable help in using a thesaurus correctly and reaching a correct understanding of the given field of knowledge. Term relationships are links between terms that often describe synonyms, near-synonyms, or hierarchical relations. Synonyms and near-synonyms are indicated by a Related Term (RT). The way the term "Cybernetics" is related to the term "Computers" is an example of such a relationship. Hierarchical relationships are used to indicate terms which are narrower and broader in scope. A Broader Term (BT) is a more general term, e.g. "Apparatus" is a generalization of "Computers". Reciprocally, a Narrower Term (NT) is a more specific term, e.g. "Digital Computer" is a specialization of "Computer". BT and NT are reciprocals; a broader term necessarily implies at least one other term which is narrower. Thesaurus designers are generally careful to ensure that BT and NT indicate class relationships, as distinguished from part-whole relationships. Some thesauri also include Use (USE) and Used For (UF) indicators when an authorized term is to be used for another, unauthorized, term; for example the entry for the authorized term "Frequency" could have the indicator "UF Pitch". Reciprocally, the entry for the unauthorized term "Pitch" would have the indicator "USE …
subclass of: Structured knowledge resource
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has definition source: Wikipedia defSource
example: Unified Medical Language System (UMLS)

Ontology
type: Class
definition: In both computer science and information science, an ontology represents a set of concepts within a domain and the relationships between those concepts. It is used to reason about the objects within that domain. Ontologies are used in artificial intelligence, the semantic web, software engineering, biomedical informatics and information architecture as a form of knowledge representation about the world or some part of it. Ontologies generally describe: * Individuals: the basic or "ground level" objects * Classes: sets, collections, or types of objects[1] * Attributes: properties, features, characteristics, or parameters that objects can have and share * Relations: ways that objects can be related to one another * Events: the changing of attributes or relations
subclass of: Structured knowledge resource
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has definition source: Wikipedia defSource
nif ID: _4_8.1
example: Basic Formal Ontology (BFO)
example: BIRNLex
example: Descriptive Ontology for Linguistic and Cognitive Engineering (DOLCE)
example: Formal Model of Anatomy (FMA)
example: Gene Ontology (GO)
example: OBO Ontology of Phenotypic Qualities (PATO)
example: OBO Relations Ontology (OBO-RO)
example: Subcellular Anatomy Ontology (SAO)

Research knowledgebase
type: Class
synonym: Basic research knowledge base
synonym: Knowledge base
synonym: Knowledgebase
synonym: Research knowledge base
definition: Basic research knowledge base
subclass of: Structured knowledge resource
created date: 2007-10-09
modified date: September 10, 2009
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _1_1.3
temp definition: A collection research data arranged according to a structured semantic framework.

Clinical knowledgebase
type: Class
synonym: Clinical knowledge base
synonym: Clinical research (translational) knowledge base
synonym: Clinical research knowledge base
synonym: Clinical research translational knowledge base
subclass of: Structured knowledge resource
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _1_1.2.1
temp definition: A collection clinical biomedical subject data - individual records or reduced information - arranged according to a structured semantic framework. Includes diagnosis, treatment, and/or outcomes information.

License
type: Class
subclass of: birnlex_11038
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary

Open-source license
type: Class
alternative label: Open source license
synonym: Open source license
definition: An open source license is a copyright license for computer software that makes the source code available under terms that allow for modification and redistribution without having to pay the original author. Such licenses may have additional restrictions such as a requirement to preserve the name of the authors and the copyright statement within the code. One popular (and sometimes considered normative) set of open source software licenses are those approved by the Open Source Initiative (OSI) based on their Open Source Definition (OSD).
subclass of: License
created date: 2007-10-11
modified date: September 10, 2009
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _2.3_4

GNU General Public License
type: Class
definition: The GNU General Public License (GNU GPL or simply GPL) is a widely used free software license, originally written by Richard Stallman for the GNU project. The GPL is the most popular and well-known example of the type of strong copyleft license that requires derived works to be available under the same copyleft. Under this philosophy, the GPL is said to grant the recipients of a computer program the rights of the free software definition and uses copyleft to ensure the freedoms are preserved, even when the work is changed or added to. This is in distinction to permissive free software licenses, of which the BSD licenses are the standard examples.
subclass of: Open-source license
version info: 146107
created date: 2007-10-11
modified date: 2007-10-11
modified date: June 14, 2011
acronym: GPL
defining citation URI: http://www.gnu.org/licenses/gpl-2.0.html
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _2.3_4.1

GNU Lesser General Public License
type: Class
subclass of: Open-source license
created date: 2007-10-11
modified date: 2007-10-11
acronym: LGPL
defining citation URI: http://www.gnu.org/licenses/lgpl-2.1.html
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _2.3_4.2

Simulation software
type: Class
definition: A resource that provides an application or program that is based on the process of imitating a real phenomenon with a set of mathematical formulas. It is, essentially, a program that allows the user to observe an operation through simulation without actually running the program.
subclass of: birnlex_11012
subclass of: Restriction
  on property: RO_0000053
  some values from: Computational model
created date: 2007-10-11
modified date: 2007-10-11
modified date: June 11, 2011
has birnlex curator: BIRN OTF
has curation status: uncurated
nif ID: _4_15

Text-mining software
type: Class
subclass of: birnlex_11012
subclass of: Restriction
  on property: RO_0000053
  some values from: Lexical processing algorithm
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: BIRN OTF
has curation status: uncurated

Mozilla Public License
type: Class
subclass of: Open-source license
created date: 2007-10-11
modified date: 2007-10-11
acronym: MPL
defining citation URI: http://www.mozilla.org/MPL/MPL-1.1.html
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _2.3_4.2

Apache License
type: Class
subclass of: Open-source license
created date: 2007-10-11
modified date: 2007-10-11
defining citation URI: http://www.apache.org/licenses/LICENSE-2.0.html
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _2.3_4.3

BSD License
type: Class
subclass of: Open-source license
editorial note: Note as of 2006, the BSD License is equivalent to the MIT License
created date: 2007-10-11
modified date: 2007-10-11
defining citation URI: http://www.opensource.org/licenses/bsd-license.php
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _2.3_4.3

MIT License
type: Class
subclass of: Open-source license
created date: 2007-10-11
modified date: 2007-10-11
defining citation URI: http://www.opensource.org/licenses/mit-license.html
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _2.3_4.3

Closed-source license
type: Class
alternative label: Closed source license
synonym: Closed source license
synonym: Restricted license
definition: Any non open source license with restrictions on the source code.
subclass of: License
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _2.3_5

Commercial license
type: Class
subclass of: Closed-source license
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _2.3_5.1

Book
type: Class
definition: A written or printed work of fiction or nonfiction, usually on sheets of paper fastened or bound together within covers, or an electronic facsimile thereof.
subclass of: birnlex_11038
version info: 151334
created date: 2007-10-11
modified date: 2007-10-11
modified date: June 14, 2011
has birnlex curator: Bill Bug
has curation status: uncurated

Book series volume
type: Class
subclass of: birnlex_11038
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated

Personal communication
type: Class
synonym: Informal communication
subclass of: birnlex_11038
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Conference proceeding
type: Class
subclass of: birnlex_11038
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Discussion
type: Class
definition: Discussion among a group in some forum, public, private, or electronic, which may or may not be moderated, for example, a single discussion thread in a listserv (NLM).
subclass of: birnlex_11038
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Government publication
type: Class
subclass of: birnlex_11038
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Standard specification
type: Class
synonym: standard spec
synonym: standards document
subclass of: birnlex_11038
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated

National standard specification
type: Class
synonym: government standard specification
subclass of: Standard specification
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated

International standard specification
type: Class
synonym: consortium standard specification
subclass of: Standard specification
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated

birnlex 2363
type: Class
definition: Listserv or discussion group (as an entity, as opposed to a single discussion thread which uses the value "discussion") (NLM).
subclass of: birnlex_11038
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Patent
type: Class
subclass of: birnlex_11038
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Thesis
type: Class
subclass of: birnlex_11038
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Website
type: Class
subclass of: birnlex_11038
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Portal
type: Class
definition: A web portal is a site that functions as a point of access to information on the World Wide Web. Portals present information from diverse sources in a unified way. Popular portals are MSN, Yahoo, and AOL. Aside from the search engine standard, web portals offer other services such as news, stock prices, infotainment and various other features. Portals provide a way for enterprises to provide a consistent look and feel with access control and procedures for multiple applications, which otherwise would have been different entities altogether. A personal portal is a site on the World Wide Web that typically provides personalized capabilities to its visitors, providing a pathway to other content. It is designed to use distributed applications, different numbers and types of middleware and hardware to provide services from a number of different sources. In addition, business portals are designed to share collaboration in workplaces. A further business-driven requirement of portals is that the content be able to work on multiple platforms such as personal computers, personal digital assistants (PDAs), and cell phones.
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has definition source: Wikipedia defSource
nif ID: _1_5

Organization portal
type: Class
synonym: Institution portal
synonym: Institutional portal
synonym: Organizational portal
definition: A portal where either the aggregated resources are restricted to those describing or associated with the organization or access to the portal is limited to members of the organization.
subclass of: Portal
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _1_5.4

Department portal
type: Class
definition: A portal where either the aggregated resources are restricted to those describing or associated with an institutional department or access to the portal is limited to members of that department.
subclass of: Organization portal
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _1_5.3

Laboratory portal
type: Class
definition: A portal where either the aggregated resources are restricted to those describing or associated with a specific laboratory or access to the portal is limited to members of that laboratory.
subclass of: Organization portal
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _1_5.3

Topical portal
type: Class
synonym: Information portal
definition: A portal where the aggregated resources are restricted to those describing or related to a particular topic.
subclass of: Portal
created date: 2007-10-11
modified date: September 10, 2009
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _1_5.5

Disease-related portal
type: Class
definition: A portal where the aggregated resources are restricted to those describing or related to a particular disease.
subclass of: Topical portal
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated

Patient-support portal
type: Class
synonym: Patient-advocate portal
definition: A portal where the aggregated resources are restricted to those describing or related to a particular disease and are specifically targetted to provide information to the community of patients and the families of patients diagnosed with that disease.
subclass of: Disease-related portal
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated

Research forum portal
type: Class
definition: A portal where the aggregated resources are restricted to those describing or related to a particular disease and are specifically targetted to provide information to the community of basic and clinical researchers studying that specific disease.
subclass of: Disease-related portal
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
example: AlzForum
example: Schizophrenia Research Forum

Link aggregation site
type: Class
synonym: A web site containing a curated set of links typically focussed on a particular topic or set of related topics.
synonym: Link classification site
synonym: Link clustering site
subclass of: Website
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated

Citation record element
type: Class
definition: Those elements defined as a part of the PubMed DTD and used by many literature citation databases
subclass of: birnlex_11001
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM
nif ID: _4_6.2

Title set
type: Class
subclass of: Citation record element
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Abstract
type: Class
subclass of: Citation record element
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM
nif ID: _4_6.1

Author set
type: Class
subclass of: Citation record element
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Title
type: Class
synonym: primary title
subclass of: Citation record element
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Alternative title
type: Class
synonym: alt title
synonym: secondary title
subclass of: Citation record element
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Author
type: Class
subclass of: Citation record element
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Author affiliation
type: Class
synonym: author adress
subclass of: Citation record element
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Group author
type: Class
synonym: collaborative author
subclass of: Author
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Grant number
type: Class
subclass of: Citation record element
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Grant sponsor
type: Class
subclass of: Citation record element
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Citation record
type: Class
subclass of: birnlex_11001
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _4_6.2
temp definition: A collection of unstructured, scientific literature.

International Standard Book Number
type: Class
subclass of: Indentifying value
created date: 2007-10-11
modified date: 2007-10-11
acronym: ISBN
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

International Standard Serial Number
type: Class
subclass of: Indentifying value
created date: 2007-10-11
modified date: 2007-10-11
acronym: ISSN
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Serial publication element
type: Class
subclass of: Citation record element
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Volume
type: Class
subclass of: Serial publication element
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Issue
type: Class
subclass of: Serial publication element
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Serial number
type: Class
synonym: number
subclass of: Serial publication element
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Start page
type: Class
subclass of: Citation record element
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

End page
type: Class
subclass of: Citation record element
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Serial title
type: Class
synonym: Journal title
subclass of: Serial publication element
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated
has external source: NLM

Chemical compositional analysis instrument
type: Class
subclass of: birnlex_11035
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary

Chemical separation instrument
type: Class
subclass of: birnlex_11035
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary

Gel electrophoresis instrument
type: Class
subclass of: Electrophoresis instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _7_1.2

High-pressure liquid chromotography instrument
type: Class
subclass of: Liquid chromotography instrument
created date: 2007-10-11
modified date: 2007-10-11
acronym: HPLC
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _7_1.3

Liquid chromotography instrument
type: Class
subclass of: Chromotography instrument
created date: 2007-10-11
modified date: 2007-10-11
acronym: LC
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _7_1.3

Chromotography instrument
type: Class
subclass of: Chemical separation instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary

Gravity-driven liquid chromotography instrument
type: Class
subclass of: Liquid chromotography instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary

Size exclusion liquid chromotography instrument
type: Class
preferred label: Size exclusion chromotography instrument
subclass of: Gravity-driven liquid chromotography instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary

Ion-exchange liquid chromotography instrument
type: Class
preferred label: Ion-exchange chromotography instrument
subclass of: Gravity-driven liquid chromotography instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary

Agarose gel electrophoresis instrument
type: Class
subclass of: Gel electrophoresis instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary

Polyacrylamide gel electrophoresis instrument
type: Class
subclass of: Gel electrophoresis instrument
created date: 2007-10-11
modified date: 2007-10-11
acronym: PAGE
has birnlex curator: Bill Bug
has curation status: graph position temporary

Nucleic acid sequencing instrument
type: Class
synonym: sequencer
subclass of: Chemical compositional analysis instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _7_5.3

Affinity chromotography instrument
type: Class
subclass of: Gravity-driven liquid chromotography instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary

Gas chromotography instrument
type: Class
synonym: GC
subclass of: Chromotography instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary

1D polyacrylamide gel electrophoresis instrument
type: Class
subclass of: Polyacrylamide gel electrophoresis instrument
created date: 2007-10-11
modified date: 2007-10-11
acronym: 1D-PAGE
has birnlex curator: Bill Bug
has curation status: graph position temporary

2D polyacrylamide gel electrophoresis instrument
type: Class
subclass of: Polyacrylamide gel electrophoresis instrument
created date: 2007-10-11
modified date: 2007-10-11
acronym: 2D-PAGE
has birnlex curator: Bill Bug
has curation status: graph position temporary

Planar liquid chromotography instrument
type: Class
subclass of: Liquid chromotography instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary

Paper chromotography instrument
type: Class
subclass of: Planar liquid chromotography instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary

Reverse-phase high-pressure liquid chromotography instrument
type: Class
abbrev: RP-HPLC
subclass of: High-pressure liquid chromotography instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary

Thin-layer chromotography instrument
type: Class
subclass of: Planar liquid chromotography instrument
created date: 2007-10-11
modified date: 2007-10-11
acronym: TLC
has birnlex curator: Bill Bug
has curation status: graph position temporary

Mass spectrometry instrument
type: Class
subclass of: Chemical compositional analysis instrument
created date: 2007-10-11
modified date: 2007-10-11
acronym: MS
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _7_1.4

Microdialysis tubing
type: Class
subclass of: Chemical separation instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _7_1.5

Nuclear magnetic resonance instrument
type: Class
synonym: NMR instrument
subclass of: Chemical compositional analysis instrument
created date: 2007-10-11
modified date: 2007-10-11
acronym: NMR
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _7_1.6

Fraction collection instrument
type: Class
subclass of: birnlex_11035
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: uncurated

Calorimetry instrument
type: Class
synonym: Calorimeter
definition: Calorimetry is the science of measuring the heat of chemical reactions or physical changes. Calorimetry involves the use of a calorimeter. The word calorimetry is derived from the Latin word calor, meaning heat. Scottish physician and scientist Joseph Black, who was the first to recognize the distinction between heat and temperature, is said to be the founder of calorimetry.[1] Indirect calorimetry calculates heat that living organisms produce from their production of carbon dioxide and nitrogen waste (frequently ammonia in aquatic organisms, or urea in terrestrial ones), OR from their consumption of oxygen. Lavoisier noted in 1780 that heat production can be predicted from oxygen consumption this way, using multiple regression. The Dynamic Energy Budget theory explains why this procedure is correct. Of course, heat generated by living organisms may also be measured by direct calorimetry, in which the entire organism is placed inside the calorimeter for the measurement.
subclass of: Chemical compositional analysis instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary
has definition source: Wikipedia defSource
nif ID: _7_1.9

Electrophoresis instrument
type: Class
subclass of: Chemical separation instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _7_1.2

Microcalorimetry instrument
type: Class
synonym: Microcalorimeter
subclass of: Calorimetry instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _7_1.9

Constant-pressure calorimetry instrument
type: Class
synonym: Constant-pressure calorimeter
subclass of: Calorimetry instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary

Constant-volume calorimetry instrument
type: Class
synonym: Constant-volume calorimeter
subclass of: Calorimetry instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary

Differential scanning calorimetry instrument
type: Class
synonym: Differential scanning calorimeter
definition: Differential scanning calorimetry or DSC is a thermoanalytical technique in which the difference in the amount of heat required to increase the temperature of a sample and reference are measured as a function of temperature. Both the sample and reference are maintained at nearly the same temperature throughout the experiment. Generally, the temperature program for a DSC analysis is designed such that the sample holder temperature increases linearly as a function of time. The reference sample should have a well-defined heat capacity over the range of temperatures to be scanned. The basic principle underlying this technique is that, when the sample undergoes a physical transformation such as phase transitions, more (or less) heat will need to flow to it than the reference to maintain both at the same temperature. Whether more or less heat must flow to the sample depends on whether the process is exothermic or endothermic. For example, as a solid sample melts to a liquid it will require more heat flowing to the sample to increase its temperature at the same rate as the reference. This is due to the absorption of heat by the sample as it undergoes the endothermic phase transition from solid to liquid. Likewise, as the sample undergoes exothermic processes (such as crystallization) less heat is required to raise the sample temperature. By observing the difference in heat flow between the sample and reference, differential scanning calorimeters are able to measure the amount of heat absorbed or released during such transitions. DSC may also be used to observe more subtle phase changes, such as glass transitions. DSC is widely used in industrial settings as a quality control instrument due to its applicability in evaluating sample purity and for studying polymer curing
subclass of: Calorimetry instrument
created date: 2007-10-11
modified date: 2007-10-11
acronym: DSC
has birnlex curator: Bill Bug
has curation status: graph position temporary
has definition source: Wikipedia defSource

Isothermal titration calorimetry instrument
type: Class
synonym: Isothermal titration calorimeter
definition: Isothermal Titration Calorimetry (ITC) is a biophysical technique used to determine the thermodynamic parameters of (biochemical) interactions. It is most often used to study the binding of small molecules (such as medicinal compounds) to larger macromolecules (proteins, DNA etc.). An isothermal titration calorimeter is composed of two identical cells made of a highly efficient thermal conducting material such as Hasteloy alloy or gold, surrounded by an adiabatic jacket (reviewed by O'Brien et al, 2000). Sensitive thermopile/ thermocouple circuits are used to detect temperature differences between the reference cell (filled with buffer or water) and the sample cell containing the macromolecule. Prior to addition of ligand, a constant power (<1 mW) is applied to the reference cell. This directs a feedback circuit, activating a heater located on the sample cell (VP-ITC users manual, MicroCal Inc, Northampton, MA, USA. 2001). During the experiment, ligand is titrated into the sample cell in precisely known aliquots, causing heat to be either taken up or evolved (depending on the nature of the reaction). Measurements consist of the time-dependent input of power required to maintain equal temperatures between the sample and reference cells.
subclass of: Calorimetry instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary
has definition source: Wikipedia defSource

Respirometry instrument
type: Class
synonym: Metabolic rate meter
synonym: Respiratory rate meter
synonym: Respirometer
definition: Respirometry is a general term that encompass a number of techniques for obtaining estimates of the rates of metabolism of vertebrates, invertebrates, plants, tissues, cells, or microorganisms via an indirect measure of heat production (calorimetry).
subclass of: Calorimetry instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary
has definition source: Wikipedia defSource
nif ID: _7_11.3

Chemical structural analysis instrument
type: Class
subclass of: birnlex_11035
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary

Granting agency
type: Class
synonym: Granting institution
subclass of: Institution
created date: 2007-10-14
modified date: 2007-10-14
has birnlex curator: Bill Bug
has curation status: graph position temporary

Government granting agency
type: Class
synonym: Government granting institution
subclass of: Granting agency
created date: 2007-10-14
modified date: 2007-10-14
has birnlex curator: Bill Bug
has curation status: graph position temporary

United States Department of Health and Human Services granting agency
type: Class
equivalent class: Class
  one of: Center for Disease Control and Prevention
  one of: Food and Drug Administration
  one of: Agency for Healthcare Research and Quality
  one of: Agency for Toxic Substances and Disease Registry
  one of: Health Resources and Services Administration
  one of: Substance Abuse and Mental Health Services Administration
  one of: National Institutes of Health
synonym: United States Department of Health and Human Services granting institution
abbrev: US HHS Institute
subclass of: Government granting agency
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
defining citation URI: http://www.hhs.gov/about/#agencies
has birnlex curator: Bill Bug
has curation status: graph position temporary

X-Ray crystallography instrument
type: Class
synonym: X-Ray diffraction instrument
definition: is the science of determining the arrangement of atoms within a crystal from the manner in which a beam of X-rays is scattered from the electrons within the crystal. The method produces a three-dimensional picture of the density of electrons within the crystal, from which the mean atomic positions, their chemical bonds, their disorder and sundry other information can be derived. The technique of single-crystal X-ray crystallography has three basic steps. The first, and often most difficult, step is to obtain an adequate crystal of the material under study. The crystal should be sufficiently large, pure in composition and regular in structure, with no large internal imperfections such as cracks or twinning. In the second step, the crystal is placed in an intense beam of X-rays, usually of a single wavelength (monochromatic X-rays), producing the regular pattern of reflections. As the crystal is gradually rotated, previous reflections disappear and new ones appear; the intensity of every spot is recorded meticulously at every orientation of the crystal. Multiple data sets may have to be collected, with each set covering slightly more than half a full rotation of the crystal and containing tens of thousands of reflection intensities. In the third step, these data are combined computationally with complementary chemical information to produce and refine a model of the arrangement of atoms within the crystal. The final, refined model, now called a crystal structure, is usually stored in a public database.
subclass of: Chemical structural analysis instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary
has definition source: Wikipedia defSource
nif ID: _7_1.8

Chemical quantification instrument
type: Class
subclass of: birnlex_11035
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary

Radiation detection instrument
type: Class
synonym: Radioassay instrument
subclass of: Chemical quantification instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary
nif ID: _7_1.7

Scintillation detection instrument
type: Class
synonym: Scintillation counter
definition: A scintillation counter measures ionizing radiation. The sensor, called a scintillator, consists of a transparent crystal, usually phosphor, plastic (usually containing anthracene), or organic liquid (see liquid scintillation counting) that fluoresces when struck by ionizing radiation. A sensitive photomultiplier tube (PMT) measures the light from the crystal. The PMT is attached to an electronic amplifier
subclass of: Radiation detection instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary
has definition source: Wikipedia defSource

Liquid scintillation detection instrument
type: Class
synonym: Liquid scintillation counter
definition: Liquid scintillation counting is a standard laboratory method in the life-sciences for measuring radiation from beta-emitting nuclides. Scintillating materials are also used in differently constructed "counters" in many other fields. Samples are dissolved or suspended in a "cocktail" containing an aromatic solvent (historically benzene or toluene, but more recently less hazardous solvents have come into favour) and small amounts of other additives known as fluors. Beta particles emitted from the sample transfer energy to the solvent molecules, which in turn transfer their energy to the fluors; the excited fluor molecules dissipate the energy by emitting light. In this way, each beta emission (ideally) results in a pulse of light. Scintillation cocktails often contain additives that shift the wavelength of the emitted light to make it more easily detected. The samples are placed in small transparent or translucent (often glass or plastic) vials that are loaded into an instrument known as a liquid scintillation counter. The counter has two photomultiplier tubes connected in a coincidence circuit. The coincidence circuit assures that genuine light pulses, which reach both photomultiplier tubes, are counted, while spurious pulses (due to line noise, for example), which would only affect one of the tubes, are ignored. Counting efficiencies under ideal conditions range from about 30% for Tritium (a low-energy beta emitter) to nearly 100% for Phosphorus-32, a high-energy beta emitter. Some chemical compounds (notably Chlorine compounds) and highly colored samples can interfere with the counting process. This interference, known as "quenching", can be overcome through data correction or through careful sample preparation. High-energy beta emitters such as P-32 can also be counted in a scintillation counter without the cocktail. This technique, known as Cherenkov counting, relies on the Cherenkov radiation being detected directly by the photomultiplier tubes. Cherenkov count…
subclass of: Scintillation detection instrument
created date: 2007-10-11
modified date: 2007-10-11
has birnlex curator: Bill Bug
has curation status: graph position temporary
has definition source: Wikipedia defSource

National Institutes of Health granting agency
type: Class
equivalent class: Class
  one of: National Institute of Alcohol Abuse & Alcoholism
  one of: National Institute of Aging
  one of: National Institute of Allergy and Infectious Diseases
  one of: National Institute of Arthritis and Musculoskeletal and Skin Diseases
  one of: National Institute of Biomedical Imaging and Bioengineering
  one of: National Cancer Institute
  one of: National Institutes of Health Clinical Center
  one of: National Institute of Child Health and Human Development
  one of: National Institute of Deafness and Other Communication Disorder
  one of: National Institute of Dental and Cranialfacial Research
  one of: National Institute of Diabetes and Digestive and Kidney Diseases
  one of: Office of the Director of the National Institutes of Health
  one of: National Institute of Drug Abuse
  one of: National Institute of Environmental Health Sciences
  one of: National Eye Institute
  one of: National Institute of General Medical Sciences
  one of: National Heart, Lung and Blood Institute
  one of: National Human Genome Research Institute
  one of: John E. Fogarty International Center For Advanced Study in the Health Sciences
  one of: National Library of Medicine
  one of: National Institute of Mental Health
  one of: National Center on Minority Health and Health Disparities
  one of: National Institute of Neurological Disorders and Stroke
  one of: National Institute of Nursing Research
  one of: National Center for Complementary and Alternative Medicine
  one of: Center for Scientific Review
  one of: National Center for Research Resources
  one of: Womens Health Initiative
  one of: National Institutes of Health Center for Information Technology
synonym: National Institutes of Health agency
synonym: National Institutes of Health granting institution
abbrev: NIH agency
abbrev: NIH Institute
subclass of: United States Department of Health and Human Services granting agency
created date: 2007-10-14
modified date: 2007-10-14
defining citation URI: http://www.nih.gov/icd/index.html
has birnlex curator: Bill Bug
has curation status: graph position temporary

A-10 cell
type: Class
synonym: A-10
definition: The clonal cell line A10 was derived by B. Kimes and B. Brandt from the thoracic aorta of DB1X embryonic rat and possesses many of the properties characteristic of smooth muscle cells. The cells produce spontaneous action potentials at the stationary phase of the growth cycle and exhibit an increase in activity of the enzymes myokinase and creatine phosphokinase. Growth Properties: adherent
subclass of: birnlex_11036
created date: 2007-10-15
modified date: 2007-10-15
atcc ID: CRL-1476
birnlex definition: A sample of a specimen consisting of a thin plane produced through the use of a microtome or other cutting device, usually produced for the purposes of histological processing and/or microscopic examination.
has birnlex curator: Bill Bug
has curation status: uncurated

Radiographic imaging protocol
type: Class
subclass of: Imaging protocol
created date: 2007-11-20
modified date: 2007-11-20
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: An imaging protocol where images are assembled by detecting the pattern created when a particular type of radiated energy is applied to a biomaterial object.
umls cui: C0457276

Ultrasonographic imaging protocol
type: Class
synonym: Echography
synonym: Sonography
synonym: Ultrasonic imaging protocol
synonym: Ultrasonography
synonym: Ultrasound imaging procedure
synonym: Ultrasound imaging protocol
definition: * RAEB: The visualization of deep structures of the body by recording the reflections of echoes of pulses of ultrasonic waves directed into the tissues. Use of ultrasound for imaging or diagnostic purposes employs frequencies ranging from 1.6 to 10 megahertz. (MSH99) (NCI) * The visualization of deep structures of the body by recording the reflections of echoes of pulses of ultrasonic waves directed into the tissues. Use of ultrasound for imaging or diagnostic purposes employs frequencies ranging from 1.6 to 10 megahertz. (MSH) * Use of ultrasound for imaging or diagnostic purposes. Employs frequencies ranging from 1.6 to 10 megahertz. (DCTD-DIP) (NCI) * high frequency sound waves used to identify and examine internal organs and structures without the invasive hazards of X xays, dyes, or fluoroscopy. (CSP)
subclass of: Radiographic imaging protocol
disjoint with: Nuclear medicine imaging protocol
created date: 2007-11-20
modified date: 2007-11-20
has birnlex curator: Bill Bug
has curation status: uncurated
has definition source: UMLS defSource
umls cui: C0041618

Nuclear medicine imaging protocol
type: Class
synonym: NMR
subclass of: Radiographic imaging protocol
created date: 2007-11-20
modified date: 2007-11-20
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
umls cui: C0024485

Planar imaging protocol
type: Class
subclass of: Nuclear medicine imaging protocol
disjoint with: Cross-sectional nuclear imaging protocol
created date: 2007-11-20
modified date: 2007-11-20
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated

Cross-sectional nuclear imaging protocol
type: Class
subclass of: Nuclear medicine imaging protocol
created date: 2007-11-20
modified date: 2007-11-20
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated

Client program
type: Class
synonym: software client
subclass of: Data access protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: BIRN OTF
has curation status: uncurated
nif ID: _2.2_3

Multiple electrode extracellular recording protocol
type: Class
subclass of: Extracellular electrode recording protocol
created date: 2007-10-09
modified date: 2007-10-09
has birnlex curator: Bill Bug
has curation status: uncurated
nif ID: _7_3.1.2

Affective assessment
type: Class
definition: An neuropsychiatric instrument consisting of a series of patient-answer and/or clinician-answered questions designed to assess the affective state of the patient. Typically score ranges are mapped to particular stages or states along an affective continuum such as depressive state.
subclass of: Mental state assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has curation status: uncurated

Genetic assessment
type: Class
definition: A evaluative instrument collecting together either individual and/or pedigree related questions and/or data values all designed to evaluate the dependence of a particular trait or disorder on genetic variability.
subclass of: Assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has curation status: uncurated

Socio-demographic assessment
type: Class
definition: A evaluative instrument collecting together either individual and/or family related questions and/or data values all designed to evaluate the dependence of a particular trait or disorder on social, economic and/or familial environmental factors.
subclass of: Assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has curation status: uncurated

Mental state assessment
type: Class
definition: An neuropsychiatric instrument consisting of a series of patient-answer and/or clinician-answered questions designed to assess the mental state of the patient. Typically score ranges are mapped to particular stages or states along a continuum such as depressive state.
subclass of: Assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has curation status: uncurated

Movement control assessment
type: Class
definition: A behavioral instrument consisting of a series of patient-answer and/or clinician-answered questions along with metrics for performing specific movement related tasks both voluntary and involuntary designed to assess the state of the patients pyramidal, extrapyramidal, and reflex movement pathways.
subclass of: Behavioral assessment
version info: 124753
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has curation status: uncurated

Abnormal Involuntary Movement Scale
type: Class
abbrev: AIMS
definition: The AIMS is an assessment of movement dysfunctions. It is a 12-item instrument assessing abnormal involuntary movements associated with antipsychotic drugs, such as tardive dystonia and chronic akathisia, as well as 'spontaneous' motor disturbance related to the illness itself. Scoring the AIMS consists of rating the severity of movement in three main anatomic areas (facial/oral, extremities, and trunk), based on a five-point scale (0=none, 4=severe).
subclass of: Movement control assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: National Institute of Mental Health. Abnormal Involuntary Movement Scale. In Guy, W., ed. (1976). ECDEU Assessment Manual. Washington DC, U.S. Department of Health, Education, and Welfare: 534.
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0450978

Anxiety Status Inventory
type: Class
abbrev: ASI
definition: The AIS is an assessment of anxiety, consists of 20 somatic and affective symptoms of anxiety. Each item is rated on severity from 1 to 4, where 1 indicates none and 4 indicates severe. The raw score range is from 20 - 80. This is converted to a percentage, by dividing the raw score by 80 and multiplying by 100. Low scores or percentages indicate low levels of anxiety and high scores indicate high levels of anxiety.
subclass of: Affective assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Zung, W.W.K. (1971). A rating instrument for anxiety disorders. Psychosomatics, 8, 6, 371-379.
defining citation ID: PMID:5172928
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0451594

Barnes Akathisia Rating Scale
type: Class
abbrev: Barnes
definition: The Barnes Akathisia Rating Scale is an assessment of akathisia which is a movement dysfunction. It is a four-item scale to assess the presence and severity of drug-induced akathisia. It is the most widely used comprehensive rating scale for akathisia, including both objective items (eg observed restlessness) and subjective items (eg patient's awareness of restlessness and related distress), together with a global clinical assessment of akathisia. Global assessment is made on a scale of 0 to 5 with comprehensive definitions provided for each anchor point on scale: 0=absent; 1=questionable; 2=mild akathisia; 3=moderate akathisia; 4=marked akathisia; 5=severe akathisia.
subclass of: Movement control assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Barnes, T.R. (1989). A rating scale for drug-induced akathisia. British Journal of Psychiatry, 154, 672-676.
defining citation ID: PMID: 2574607
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0450978
usage note: Note that akathisia is listed in BIRNLex as Psychomotor Aggitation (birnlex_12661) which is the prefered term given in MeSH (BB).

Beck Depression Inventory
type: Class
abbrev: BDI
definition: A survey completed by a patient, with each answer scored on a scale of 0 to 3, designed to measure presence of depression. (NCI)
subclass of: Affective assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Beck, A. T., Steer, R..A., Garbin, M.. G., (1988) Psychometric properties of the Beck Depression Inventory: Twenty-five years of evaluation. Clinical Psychology Review 8 (1), 77-100.
defining citation: Beck, A.T., Rial, W. Y., Rickets, K. (1974). Short form of Depression Inventory: Cross-validation. Psychological-Reports 34 (3), 1184-1186.
defining citation: Beck, A.T., Ward, C. H., Mendelson, M., Mock, J., & Erbaugh, J. (1961). An inventory for measuring depression. Archives of General Psychiatry 4, 561-571.
defining citation ID: PMID: 4424377
defining citation ID: PMID: 13688369
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0451022

Calgary Depression Scale
type: Class
abbrev: CDSS
definition: The CDSS is an assessment of depression in schizophrenia. It has been extensively evaluated in both relapsed and remitted patients and appears sensitive to change. In comparison to the Hamilton Depression Scale, it has fewer factors and less overlap with positive and negative symptoms. This lack of overlap is present both at the time of relapse and at the time of remission
subclass of: Affective assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Addington, D., Addington, J., Maticka-Tyndale, E., & Joyce, J. (1992). Reliability and validity of a depression rating scale for schizophrenics. Schizophrenia Research, 6, 201-208.
defining citation ID: PMID: 1571313
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary

Deficit Syndrome Score Sheet
type: Class
abbrev: SDS
definition: The SDS is a symptom assessment tool, which assesses negative symptoms in schizophrenia. Six core items of the deficit syndrome (restricted affect; diminished emotional range; poverty of speech; curbing of interests; diminished sense of purpose; and diminished social drive) are rated on a 5-point scale, 0=absent; 1=mild; 2=moderate; 3=severe; 4=very severe. Each item is also rated as to whether it is a primary symptom and a stable symptom (yes, no, n/a).
subclass of: Mental state assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Kirkpatrick, B., Buchanan, R.W., McKenney, P.D., Alphs, L.D., Carpenter, W.T. (1989). The schedule for the deficit syndrome: An instrument for research in schizophrenia. Psychiatry Research, 30, 119-123.
defining citation ID: PMID: 2616682
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary

Demographic assessment
type: Class
definition: An assessment of the statistical characterization of human populations or segments of human populations (e.g., characterization by age, sex, race, or income). (NCI)
subclass of: Socio-demographic assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0011296

Edinburgh Handedness Inventory
type: Class
definition: The Edinburgh Handedness Inventory is a 20 or 10 item questionnaire in which participants are asked to indicate the preference in the use of hands during certain activities. Participants are instructed to indicate hand preference by a single check. For activities in which they would "never try to use the other hand unless absolutely forced to", two checks should be indicated. To score the inventory, add the number of checks in each column, whichever column total is greater is considered the individual's handedness.
subclass of: Handedness assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Oldfield, R.C. (1971). The assessment and analysis of handedness: the Edinburgh inventory. Neuropsychologia, 9(1), 97-113.
defining citation ID: PMID: 5146491
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary

Education assessment
type: Class
synonym: education
definition: Assessment of a demographic parameter indicating the number of years of schooling or the highest level of achievement at school. (NCI); Assessment of educational attainment or level of education of individuals. (MSH)
subclass of: Socio-demographic assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0013658

Ethnicity assessment
type: Class
synonym: ethnicity
definition: Assessment of an individual's cultural heritage that sets them apart from others in a variety of social relationships. (MSH); Assessment of an individual's social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Assessment of an individual's ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI);
subclass of: Socio-demographic assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C1287117

Ethnicity
type: Class
definition: A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (MSH); A social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI); The concept of ethnic origin is an attempt to classify people, not according to their current ethnicity, but according to where their ancestors came from. Ethnic origin has become a popular classification in statistics, where the concept of race has been largely discarded. (from Wikipedia) (NCI); a group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (CSP)
subclass of: PATO_0001241
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0438960

Family Interview for Genetics Studies
type: Class
abbrev: FIGS
definition: The FIGS is structured interview for gathering diagnostic information about relatives in the pedigree being studied. FIGS data are collected from everyone interviewed about all known members of the extended family. A pedigree (including at a minimum the proband, his/her parents, grandparents, siblings, aunts, uncles, offspring, and spouse) is drawn as part of the interview. The second step of the FIGS is to ask the General Screening Questions. The third step is to complete a Face Sheet and Symptom Checklists with selected relatives.
subclass of: Genetic assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Maxwell, M.E.: Manual for the FIGS (Family Interview for Genetics Studies). Bethesda, Md, National Institute of Mental Health, Clinical Neurogenetics Branch, Intramural Research Program, 3/30/1992
defining citation ID: PMID: 2616682
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary

Camberwell FamilyInterview
type: Class
abbrev: CFI
definition: CFI is used to determine whether a person or family has high expressed emotion or low expressed emotion through a taped interview known as the Camberwell Family Interview. Answers to questions and non-verbal cues are used to determine if some one has high expressed emotion. There is another measurement that is taken from the view of the patient. It rates the patient's perception of how his family feels about him and the disorder. If the patient feels that the parents are too protective or not caring the patient feels that his parents don't care of his independence or trust his judgement. The three dimensions of high EE shown are hostility, emotional over-involvement and critical comments.
subclass of: Family Interview for Genetics Studies
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Vaughn C, Leff J. (1976) The measurement of expressed emotion in the families of psychiatric patients. Br J Soc Clin Psychol. Jun;15(2):157-65.
defining citation ID: PMID: 938822
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0451057

Familial member assessment
type: Class
definition: Assessment of status of familial relation of patient under study.
subclass of: Socio-demographic assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has curation status: graph position temporary

Paternal assessment
type: Class
definition: Assessment of status of the father of patient under study.
subclass of: Familial member assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has curation status: graph position temporary

Maternal assessment
type: Class
definition: Assessment of status of the mother of patient under study.
subclass of: Familial member assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has curation status: graph position temporary

Father's education
type: Class
definition: Assessment of an individual's father's demographic parameter indicating the number of years of schooling or the highest level of achievement at school. (NCI); Assessment of an individual's father's educational attainment or level of education of individuals. (MSH)
subclass of: Paternal assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary

Father's occupation
type: Class
definition: An assessment of an individual's father's work specialties as defined by duties and required skills. Use a more specific term if possible. (PSY); An assessment of an individual's father's crafts, trades, professions, or other means of earning a living. (MSH); An assessment an individual's father's principal activity that a person does to earn money. (NCI)
subclass of: Paternal assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0237754

Mother's education
type: Class
definition: Assessment of an individual's mother's demographic parameter indicating the number of years of schooling or the highest level of achievement at school. (NCI); Assessment of an individual's mother's educational attainment or level of education of individuals. (MSH)
subclass of: Maternal assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary

Father's occupation
type: Class
definition: An assessment of an individual's mother's work specialties as defined by duties and required skills. Use a more specific term if possible. (PSY); An assessment of an individual's mother's crafts, trades, professions, or other means of earning a living. (MSH); An assessment an individual's mother's principal activity that a person does to earn money. (NCI)
subclass of: Maternal assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0237754

Favorites assessment
type: Class
synonym: favorites
definition: An assessment of an indivdual's preferred category exemplars. Assessed on items such as food, color, tv show, etc. Typically used for regression testing of databases.
subclass of: Mental state assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Kirkpatrick, B., Buchanan, R.W., McKenney, P.D., Alphs, L.D., Carpenter, W.T. (1989). The schedule for the deficit syndrome: An instrument for research in schizophrenia. Psychiatry Research, 30, 119-123.
defining citation ID: PMID: 2616682
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary

Gender assessment
type: Class
synonym: gender
definition: An assessment of gender, the assemblage of properties that distinguish people on the basis of their societal roles. (NCI) An assessment of gender, the socially-constructed identity of male or female. (MSH); An assessment of the sex of an organism.(BIRNLex).
subclass of: Socio-demographic assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C1287419

Hallucination assessment
type: Class
synonym: hallucination
definition: An assessment of a hallucination, a false sensory perception in the absence of an external stimulus, as distinct from an illusion which is a misperception of an external stimulus. (from Wikipedia) (NCI); An assessment of hallucinations, subjectively experienced sensations in the absence of an appropriate stimulus, but which are regarded by the individual as real. They may be of organic origin or associated with MENTAL DISORDERS. (MSH); An assessment of hallucinations, subjectively experienced sensations in the absence of an appropriate stimulus, but which are regarded by the individual as real; may be of organic origin, drug induced, or associated with a mental disorder. (CSP)
subclass of: Mental state assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0018524

Handedness assessment
type: Class
definition: Assessment of behavioral manifestations of cerebral dominance in which there is preferential use and superior functioning of either the left or the right side, as in the preferred use of the right hand or right foot. (MSH); Assessment of learned or spontaneous differential dexterity with and tendency to use one hand rather than the other. (PSY); Assessment of the preferential use of the hand of one side in voluntary motor acts. (CSP)
subclass of: Behavioral assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C1286612

InterSePT Scale for Suicidal Thinking
type: Class
abbrev: InterSEPT
definition: The InterSePT Scale for Suicidal Thinking (ISST) is an assessment of current suicidal ideation in patients with schizophrenia and schizoaffective disorders.
subclass of: Mental state assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Lindenmayer, J. P., Czobor, P., Alphs, L., Nathan, A., Anand, R., Islam, Z., Chou J.C.Y. & InterSePT Study Group. (2003). The InterSePT scale for suicidal thinking reliability and validity. Schizophrenia Research, 63,1,161-170.
defining citation ID: PMID: 12892870
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary

Living arrangement assessment
type: Class
synonym: living arrangement
definition: An assessment of the manner in which an individual habitates, with particular reference to whom living space is shared (e.g., spouse, children, significant other, friend, other family member(s)).
subclass of: Socio-demographic assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0242487

Marital status assessment
type: Class
synonym: marital status
definition: Assessment of a demographic parameter indicating a person's conjugal status. Marital status categories include married, divorced, widowed, or never married. (NCI); Assessment of a demographic parameter indicating a person's status with respect to marriage, divorce, widowhood, singleness, etc. (MSH)
subclass of: Familial member assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0024819

Positive and Negative Symptom Scale
type: Class
abbrev: PANSS
definition: The PANSS is an assessment of positive and negative symptoms in schizophrenia. It is a 30-item rating instrument evaluating the presence/absence and severity of positive, negative and general psychopathology of schizophrenia. The scale was developed from the BPRS and the Psychopathology Rating Scale. All 30 items are rated on a 7-point scale (1=absent; 7=extreme).
subclass of: Mental state assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Kay, S.R., Opler, L.A., & Fiszbein, A. (1987) The positive and negative syndrome scale (PANSS) for schizophrenia. Schizophrenia Bulletin, 13, 261-276.
defining citation ID: PMID: 3616518
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0871099

Modified Positive and Negative Symptom Scale
type: Class
abbrev: Modified PANSS
definition: These 4 questions in conjunction with the SANS and SAPS provide the answers to the PANSS assessment.
subclass of: Positive and Negative Symptom Scale
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Kay, S.R., Opler L.A. and Fiszbein, A. (1992) Positive and negative syndrome scale (PANSS) rating manual, Multihealth Systems, Inc., Toronto, Canada.
defining citation: Kay, S.R., Opler, L.A., & Fiszbein, A. (1987) The positive and negative syndrome scale (PANSS) for schizophrenia. Schizophrenia Bulletin, 13, 261-276.
defining citation ID: PMID: 3616518
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary

North American Adult Reading Test
type: Class
abbrev: NAART
definition: The North American Adult Reading Test (NAART) is an assessment of verbal intellectual ability. The NAART is a reliable and valid measure of verbal intelligence, comparable in psychometric properties to the WAIS-R Vocabulary test and with equal psychometric properties in young, middle-aged and older adults. Each incorrectly pronounced word is counted as one error, score range is from 0 to 60, with 0 indicating no pronunciation errors and 60 indicating pronunciation errors on all items.
subclass of: Neuropsychological assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Nelson, H.E. & O'Connell, A. (1978). Denentia: The estimation of pre-morbid intelligence levels using the new adult reading test. Cortex, 14, 234-244.
defining citation: Nelson, H.E. (1982). National Adult Reading Test (NART): Test Manual, Windsor, U.K.: NFER nelson.
defining citation ID: PMID: 679704
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0451328

Offspring cardinality assessment
type: Class
synonym: number of children
definition: An assessment of the number of sons or daughters of any age, including biological offspring and sometimes including unborn children, adopted children, stepchildren, foster children and children born outside of marriage; person under an age specified by law. (NCI)
subclass of: Familial member assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0008059

Occupation assessment
type: Class
synonym: occupation
definition: An assessment of an individual's work specialties as defined by duties and required skills. Use a more specific term if possible. (PSY); An assessment of an individual's crafts, trades, professions, or other means of earning a living. (MSH); An assessment of the principal activity that a person does to earn money. (NCI)
subclass of: Familial member assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0028811

Developmental assessment
type: Class
definition: A evaluative instrument collecting together either subject and/or clinician-answered questions related to evaluating the developmental stage of the subject.
subclass of: Assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has curation status: uncurated

Premorbid Adjustment Scale
type: Class
abbrev: PAS
definition: The Premorbid Adjustment Scale (PAS) is a rating scale for use in schizophrenia. It evaluates the degree of achievement of developmental goals at each of several periods of a subject's life before the onset of schizophrenia
subclass of: Developmental assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Cannon-Spoor,H. E., Potkin, S.G. & Wyatt, R. J. (1982) Measurement of premorbid adjustment in chronic schizophrenia. Schizophrenia Bulletin, 8, 470-484.
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary

Quick mood scale
type: Class
abbrev: CDSS
definition: The Quick Mood Scale is a 12-item category scale which gives information on six factors of importance in the assessment of drug effects on the central nervous system (drowsiness, anxiety, depression, aggression, confusion and lack of coordination). Responders are instructed to give an indication of his or her mood at this moment for each of the 12 items on a 5 point likert scale (not at all, a little, moderately, very, extremely).
subclass of: Affective assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Woodruffe-Peacock, C., Turnbull, G.M., Johnson, M.A., Elahi, N., Preston, G.C. (1998). The quick mood scale: development of a simple mood assessment for clinical pharmacology studies. Human Psychopharmacology, 13, 53-88.
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary

Race assessment
type: Class
synonym: race
definition: An assessment of an individual's race - an arbitrary classification of taxonomic group that is a division of a species; usually arise as a consequence of geographical isolation within a species and characterised by shared heredity, physical attributes and behavior, and in case of humans, by common history, nationality, or geographic distribution. (NCI)
subclass of: Socio-demographic assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0034510

Scale for the Assessment of Negative Symptoms
type: Class
abbrev: SANS
definition: The SANS is an assessment of negative symptoms in schizophrenia. It assesses five symptom complexes to obtain clinical ratings of negative symptoms in patients with schizophrenia. They are: affective blunting; alogia (impoverished thinking); avolition/apathy; anhedonia/asociality; and disturbance of attention. Assessments are conducted on a six-point scale (0=not at all to 5=severe). Ratings are made on each negative symptom cluster, after consideration has been given to each of the items contained within the various complex scores. Item descriptions are not given, but anchor point descriptions are given for each score.
subclass of: Mental state assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Andreasen, N. C. (1983). The Scale for the Assessment of Negative Symptoms (SANS). Iowa City, Iowa: The University of Iowa, 1983.
defining citation: Andreasen, N.C. & Olsen, S. (1982). Negative v positive schizophrenia: definition and validation. Archives of General Psychiatry, 39, 789-794.
defining citation ID: PMID: 7165478
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0451383

Structured clinical interview for DSM-IV Axis I Disorders
type: Class
abbrev: SCID-I
definition: * The SCID is a diagnostic tool. It assesses thirty-three of the more commonly occurring psychiatric disorders described in the DSM-IV. The SCID is a semi-structured interview that allows the experienced clinician to tailor questions to fit the patient's understanding; to ask additional questions that clarify ambiguities; to challenge inconsistencies; and to make clinical judgments about the seriousness of symptoms. The main uses of the SCID are for diagnostic evaluation, research, and the training of mental-health professionals. (BIRNLex) * The Structured Clinical Interview for DSM-IV Axis I Disorders (SCID-I) is a semi-structured interview for making the major DSM-IV Axis I diagnoses. The SCID-II is a semi-structured interview for making DSM-IV Axis II: Personality Disorder diagnoses (www.scid4.org/faq/scidfaq.html).
subclass of: Mental state assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: First, M.B., Spitzer, R.L., Gibbon, M., & Williams, J.B., SCID-I/Scoresheet, Clinician version, American Psychiatric Press, Inc. 1-6
defining citation: First, M.B., Spitzer, R.L., Gibbon, M., & Williams, J.B.W. (1997). Structured Clinical Interview for DSM-IV Axis I Disorders (SCID-I), Clinician Version. American Psychiatric Press, Washington, DC.
defining citation: R.L. Spitzer, J.B.W. Williams, M. Gibbon and M.B. First, The structured clinical interview for DSM-III-R (SCID), Arch Gen Psychiatry 49 (1992), pp. 624-629.
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0935589

Structured clinical interview for DSM-IV Axis I Disorders - non-patient
type: Class
abbrev: SCID-I-NP
definition: * The SCID is a diagnostic tool. It assesses thirty-three of the more commonly occurring psychiatric disorders described in the DSM-IV. The SCID is a semi-structured interview that allows the experienced clinician to tailor questions to fit the patient's understanding; to ask additional questions that clarify ambiguities; to challenge inconsistencies; and to make clinical judgments about the seriousness of symptoms. The main uses of the SCID are for diagnostic evaluation, research, and the training of mental-health professionals. (BIRNLex) * The Structured Clinical Interview for DSM-IV Axis I Disorders (SCID-I) is a semi-structured interview for making the major DSM-IV Axis I diagnoses. The SCID-II is a semi-structured interview for making DSM-IV Axis II: Personality Disorder diagnoses (www.scid4.org/faq/scidfaq.html). * SCID non-patient (overview and screening module) modified by Stanford University, 9/27/1999
subclass of: Mental state assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: First, M.B., Spitzer, R.L., Gibbon, M., & Williams, J.B., SCID-I/Scoresheet, Clinician version, American Psychiatric Press, Inc. 1-6
defining citation: First, M.B., Spitzer, R.L., Gibbon, M., & Williams, J.B.W. (1997). Structured Clinical Interview for DSM-IV Axis I Disorders (SCID-I), Clinician Version. American Psychiatric Press, Washington, DC.
defining citation: R.L. Spitzer, J.B.W. Williams, M. Gibbon and M.B. First, The structured clinical interview for DSM-III-R (SCID), Arch Gen Psychiatry 49 (1992), pp. 624-629.
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary

Structured clinical interview for DSM-IV Axis I Disorders - patient
type: Class
abbrev: SCID-I-P
definition: * The SCID is a diagnostic tool. It assesses thirty-three of the more commonly occurring psychiatric disorders described in the DSM-IV. The SCID is a semi-structured interview that allows the experienced clinician to tailor questions to fit the patient's understanding; to ask additional questions that clarify ambiguities; to challenge inconsistencies; and to make clinical judgments about the seriousness of symptoms. The main uses of the SCID are for diagnostic evaluation, research, and the training of mental-health professionals. (BIRNLex) * The Structured Clinical Interview for DSM-IV Axis I Disorders (SCID-I) is a semi-structured interview for making the major DSM-IV Axis I diagnoses. The SCID-II is a semi-structured interview for making DSM-IV Axis II: Personality Disorder diagnoses (www.scid4.org/faq/scidfaq.html). * SCID non-patient (overview and screening module) modified by Stanford University, 9/27/1999
subclass of: Mental state assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: First, M.B., Spitzer, R.L., Gibbon, M., & Williams, J.B., SCID-I/Scoresheet, Clinician version, American Psychiatric Press, Inc. 1-6
defining citation: First, M.B., Spitzer, R.L., Gibbon, M., & Williams, J.B.W. (1997). Structured Clinical Interview for DSM-IV Axis I Disorders (SCID-I), Clinician Version. American Psychiatric Press, Washington, DC.
defining citation: R.L. Spitzer, J.B.W. Williams, M. Gibbon and M.B. First, The structured clinical interview for DSM-III-R (SCID), Arch Gen Psychiatry 49 (1992), pp. 624-629.
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary

Scale for the Assessment of Positive Symptoms
type: Class
abbrev: SAPS
definition: The SAPS is an assessment of positive symptoms in schizophrenia. It accompanies the SANS.
subclass of: Mental state assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Andreasen, N. C. (1984). The Scale for the Assessment of Positive Symptoms (SAPS). Iowa City, Iowa: The University of Iowa, 1984.
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary

Self-rating Anxiety Scale
type: Class
abbrev: SAS
definition: The Self-rating Anxiety Scale is a self-administered assessment of anxiety, consisting of 20 statements. The subject is instructed to rate how each statement applies to him or her within the past week. Each item is rated on a scale from None of the time, some of the time, a good part of the time, most or all of the time. The raw score range is from 20 - 80. This is converted to a percentage, by dividing the raw score by 80 and multiplying by 100. Low scores or percentages indicate low levels of anxiety and high scores indicate high levels of anxiety.
subclass of: Affective assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Zung, W.W.K. (1971). A rating instrument for anxiety disorders. Psychosomatics, 12, 6, 371-379.
defining citation ID: PMID: 5172928
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0451595

Simpson Angus Rating Scale
type: Class
abbrev: SAS
definition: The SAS is a 10-item instrument used to evaluate the presence and severity of parkinsonian symptomatology. It is the most commonly used rating scale for Parkinsonism in clinical trials over the past 25 years. The ten items focus on rigidity rather than bradykinesia, and do not assess subjective rigidity or slowness. Items are rated for severity on a 0-4 scale, with definitions given for each anchor point.
subclass of: Movement control assessment
created date: 2008-03-14
modified date: 2008-03-14
defining citation: Simpson G.M., Angus, J.W.S.(1970). A rating scale for extrapyramidal side effects. Acta Psychiatry Scand (Suppl), 212, 11-19.
defining citation ID: PMID: 4917967
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0450978
usage note: Note that akathisia is listed in BIRNLex as Psychomotor Aggitation (birnlex_12661) which is the prefered term given in MeSH (BB).

Socio-Economic Status
type: Class
abbrev: SES
definition: The SES assessment is a demographic measure which rates a person's socio-economic status by scoring the education and occupation levels of a patient and his/her primary and secondary caretakers
subclass of: Socio-demographic assessment
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has birnlex curator: Michele Diaz
has curation status: graph position temporary
umls cui: C0086996
usage note: Note that akathisia is listed in BIRNLex as Psychomotor Aggitation (birnlex_12661) which is the prefered term given in MeSH (BB).

Cardinality value
type: Class
subclass of: birnlex_11004
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: a type of quantitative value specifying the count of another entity.

Number of b values
type: Class
definition: number of distinct b-values used
subclass of: DTI imaging protocol attribute
change note: Moved as a subclass of 'DTI imaging protocol attribute' from 'Cardinality value'.
created date: 2008-03-14
modified date: 2008-03-14
modified date: February 9, 2009
has birnlex curator: Bill Bug
has birnlex curator: Karl Helmer
has curation status: graph position temporary
has former parent class: birnlex_3049

Number of diffusion-weighted directions
type: Class
definition: the number of gradient amplitude vectors used in each complete set of diffusion-weighted data
subclass of: DTI imaging protocol attribute
change note: Moved as a subclass of 'DTI imaging protocol attribute' from 'Cardinality value'.
created date: 2008-03-14
modified date: 2008-03-14
modified date: February 9, 2009
has birnlex curator: Bill Bug
has birnlex curator: Karl Helmer
has curation status: graph position temporary
has former parent class: birnlex_3049

Number b=0 volumes
type: Class
definition: number of imaging volumes acquired without any diffusion-weighting gradients applied
subclass of: DTI imaging protocol attribute
change note: Moved as a subclass of 'DTI imaging protocol attribute' from 'Cardinality value'.
created date: 2008-03-14
modified date: 2008-03-14
modified date: February 9, 2009
has birnlex curator: Bill Bug
has birnlex curator: Karl Helmer
has curation status: graph position temporary
has former parent class: birnlex_3049

Number of b NE 0 volumes
type: Class
definition: number of diffusion-weighted directions multiplied by the number of non-zero b-values
subclass of: DTI imaging protocol attribute
change note: Moved as a subclass of 'DTI imaging protocol attribute' from 'Cardinality value'.
created date: 2008-03-14
modified date: 2008-03-14
modified date: February 9, 2009
has birnlex curator: Bill Bug
has birnlex curator: Karl Helmer
has curation status: graph position temporary
has former parent class: birnlex_3049

Event-related design
type: Class
subclass of: birnlex_11008
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
temp definition: An experimental design in which the conditions of interest are brief, and the time course is modeled as a sudden on and off-set rather than a constant state.

Independent Components Analysis
type: Class
abbrev: ICA
definition: A computational method for separating a multivariate signal into additive subcomponents supposing the mutual statistical independence of the non-Gaussian source signals. It is a special case of blind source separation. (from Wikipedia).
subclass of: birnlex_11009
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
example: Applied to fMRI data, it identifies independent temporal and spatial patterns.

General Linear Model
type: Class
abbrev: GLM
definition: The general linear model (GLM) is a statistical linear model. It may be written as Y = XB + U where Y is a matrix with series of multivariate measurements, X is a matrix that might be a design matrix, B is a matrix containing parameters that are usually to be estimated and U is a matrix containing errors or noise. The residual is usually assumed to follow a multivariate normal distribution. If the residual is not a multivariate normal distribution, generalized linear models may be used to relax assumptions about Y and U. The general linear model incorporates a number of different statistical models: ANOVA, ANCOVA, MANOVA, MANCOVA, ordinary linear regression, t-test and F-test. If there is only one column in Y (i.e., one dependent variable) then the model can also be referred to as the multiple regression model (multiple linear regression). Hypothesis tests with the general linear model can be made in two ways: multivariate and mass-univariate.(WIkiPedia)
subclass of: Computational model
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated

Gaussian Random Field
type: Class
abbrev: GRF
definition: A Gaussian random field is a random field involving Gaussian probability density functions of the variables. The initial conditions of physical cosmology generated by quantum mechanical fluctuations during cosmic inflation are thought to be a Gaussian random field with a nearly scale invariant spectrum.(WIkiPedia)
subclass of: birnlex_11001
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated

Region of Interest
type: Class
abbrev: ROI
definition: A Region of Interest, often abbreviated ROI, is a selected subset of samples within a dataset identified for a particular purpose. The concept of an ROI is commonly used in medical imaging. For example, the boundaries of a tumor may be defined on an image or in a volume, for the purpose of measuring its size. The endocardial border may be defined on an image, perhaps during different phases of the cardiac cycle, say end-systole and end-diastole, for the purpose of assessing cardiac function.There are three fundamentally different means of encoding an ROI: * burned in to the dataset, with a value that may or may not be outside the normal range of normally occurring values * as separate purely graphic information, such as with vector or bitmap (rasterized) drawing elements, perhaps with some accompanying plain (unstructured) text annotation * as separate structured semantic information (such as coded value types) with a set of spatial and/or temporal coordinates (WIkiPedia)
subclass of: birnlex_11001
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated
example: in a time-volume (4D dataset), the outline of an object at or during a particular time interval
example: in a volume (3D dataset), the contours or surfaces outlining an object
example: In neuroimaging, usually a cortical or subcortical area if defined anatomically, but it may be defined anatomically or functionally.
example: on a waveform (1D dataset), a time or frequency interval
example: on an image (2D dataset), the boundaries of an object

Statistical Parametric Mapping
type: Class
abbrev: SPM
definition: Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data. These ideas have been instantiated in software that is called SPM. The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG (http://www.fil.ion.ucl.ac.uk/spm/).
subclass of: birnlex_11009
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: uncurated

Spatial value
type: Class
subclass of: birnlex_11004
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: a type of quantitative value for a specific point in a multidimensional data set.

Pixel
type: Class
subclass of: Spatial value
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: a type of spatial value for a specific point in a 2D data set.

Voxel
type: Class
subclass of: Spatial value
created date: 2008-03-14
modified date: 2008-03-14
has birnlex curator: Bill Bug
has curation status: uncurated
temp definition: a type of spatial value for a specific point in a 3D data set.

Wide-field fluorescence imaging protocol
type: Class
subclass of: Light emitting optical imaging protocol
created date: 2008-05-01
modified date: 2008-05-01
has birnlex curator: Bill Bug
has curation status: uncurated

Vendor
type: Class
equivalent class: Class
  one of: FONAR
  one of: Hitachi Medical Systems
  one of: Philips Medical Systems
  one of: Siemens Medical Solutions
  one of: Toshiba Medical Systems
  one of: Varian
  one of: Bruker Biospin MRI
  one of: General Electric Medical Systems
subclass of: Institution
created date: 2007-10-16
modified date: 2007-10-16
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: pending final vetting

Positron emission tomography scanner
type: Class
synonym: PET scanner
definition: A Positron emission tomography scanner is a device used in a nuclear medicine to observe metabolic processes in the body.
subclass of: Imaging instrument
created date: 2016-02-12
defining citation URI: https://en.wikipedia.org/wiki/Positron_emission_tomography

Single-photon emission computed tomography scanner
type: Class
synonym: SPECT scanner
definition: A Single-photon emission computed tomography scanner is a device used in nuclear medicine tomographic imaging to measure perfusion in the body using gamma rays.
subclass of: Imaging instrument
created date: 2016-02-12
defining citation URI: https://en.wikipedia.org/wiki/Single-photon_emission_computed_tomography

Magnetoencephalography machine
type: Class
synonym: MEG machine
definition: A Magnetoencephalography machine is a device used in functional neuroimaging for mapping brain activity by recording magnetic fields produced by electrical currents occurring naturally in the brain, using very sensitive magnetometers..
subclass of: Imaging instrument
created date: 2016-02-12
defining citation URI: https://en.wikipedia.org/wiki/Magnetoencephalography

Electroencephalography machine
type: Class
synonym: EEG machine
definition: A Electroencephalography machine is a device used in electrophysiology to record electrical activity of the brain..
subclass of: Imaging instrument
created date: 2016-02-12
defining citation URI: https://en.wikipedia.org/wiki/Electroencephalography

Anatomical MRI protocol
type: Class
definition: An anatomical MRI protocol is a structural MRI protocol that can be used to delineate the anatomy, for example by the way of a segmentation or parcellation.
subclass of: Structural MRI protocol
created date: 2016-02-15
has definition source: UMLS defSource

Mass spectrometry assay
type: Class
synonym: Mass spectrometry
synonym: mass spectroscopy
abbrev: Mass spec
definition: A measuring method consisting of turning elements in a sample into ions, isolating them according to the ratio between the mass and charge numbers and detecting it electrically.
subclass of: birnlex_11025
created date: September 24, 2009

Immunoprecipitation assay
type: Class
synonym: Immunoprecipitation
definition: An assay by which an antigen is precipitated from solution using an antibody.
subclass of: birnlex_11025
editorial note: OBI has immunoprecipitation under "process"; we insert "assay" in between process and immunoprecipitation. Not sure what to do here.
created date: September 24, 2009
contributor: Maryann Martone

Chromatin immunoprecipitation assay
type: Class
synonym: Chromatin immunoprecipitation
definition: An assay which aims at identifying protein binding sites in genomic DNA and determining how protein may regulate gene transcription by relying on immunoprecipitation of DNA bound protein, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods.
subclass of: Immunoprecipitation assay
created date: February 12, 2010
defining citation: Ontology for BIomedical Investigation

Serial block face scanning electron microscopic imaging assay
type: Class
synonym: serial block face imaging
synonym: serial block face scanning electron microscopy
synonym: serial block face SEM
abbrev: SBFSEM
definition: Scanning electron microscopy assay that combines automated block-face imaging with serial sectioning inside the chamber of a scanning electron microscope and uses backscattering contrast to visualize the heavy-metal staining of tissue (adapted from Denk and Horstmann, PLoS Biol. 2004 Nov;2(11):e329, 2004).
subclass of: Scanning electron microscopic imaging assay
created date: October 20, 2012
contributor: Maryann Martone
defining citation: Denk W & Horstmann H (2004) Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biol 2: e329

Scanning electron microscopic imaging assay
type: Class
synonym: Scanning electron microscopy
abbrev: SEM
description: Electron microscopic imaging assay where the image is formed by scanning an electron beam across a sample in a scanning electron microscope, and collecting scattered electrons to form an image. The signals result from interactions of the electron beam with atoms at or near the surface of the sample. In the most common or standard detection mode, secondary electron imaging or SEI, the SEM can produce very high-resolution images of a sample surface, revealing details about less than 1 to 5 nm in size. Due to the very narrow electron beam, SEM micrographs have a large depth of field yielding a characteristic three-dimensional appearance useful for understanding the surface structure of a sample. (adapted from Wikipedia; http://en.wikipedia.org/wiki/Scanning_electron_microscopy)
subclass of: Electron microscopic imaging assay
created date: October 20, 2012
contributor: Maryann Martone

Computer Axial Tomography imaging assay
type: Class
synonym: CAT scan
synonym: CT imaging
synonym: CT scan
subclass of: birnlex_11026
subclass of: Restriction
  on property: BFO_0000055
  some values from: Neuroimaging role
version info: 190780
created date: October 20, 2012
contributor: Maryann Martone

Neuroimaging
type: Class
equivalent class: Class
  intersection of: birnlex_11025
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Neuroimaging role
description: Includes the use of various techniques to either directly or indirectly image the structure, function/pharmacology of the brain. It is a relatively new discipline within medicine and neuroscience/psychology. - definition adapted from Wikipedia
version info: 199140
created date: October 20, 2012
contributor: Anita Bandrowski

Functional neuroimaging
type: Class
synonym: Functional Brain Imaging
synonym: Functional imaging
description: Methods for visualizing REGIONAL BLOOD FLOW, metabolic, electrical, or other physiological activities in the CENTRAL NERVOUS SYSTEM using various imaging modalities. (MeSH)
subclass of: Neuroimaging
version info: 199947
created date: October 20, 2012
contributor: Andrea Arnaud

Animation software
type: Class
definition: A resource that provides an application or program that is used to rapidly display a sequence of images of 2-D or 3-D artwork or model positions in order to create an illusion of movement.
subclass of: birnlex_11012
version info: 90659
created date: September 10, 2009
modified date: June 12, 2011

Data distribution software
type: Class
alternative label: Data compression software
definition: A resource that provides an application or program that is middleware for distributed systems to standardize a data-centric publish-subscribe programming model.
subclass of: Data processing software
version info: 90662
created date: September 10, 2009
modified date: June 12, 2011

Data storage software
type: Class
definition: A resource that provides an application or program that is used to obtain a permanent holding place for digital data, until purposely erased.
subclass of: Data processing software
created date: September 10, 2009

Data transfer software
type: Class
definition: A resource that provides an application or program that is used to transfer data from point-to-point often represented as an electro-magnetic signal over a physical point-to-point or point-to-multipoint communication channel. An example of such channels are wireless communication channels.
subclass of: Data processing software
created date: September 13, 2009

Community building portal
type: Class
synonym: Community portal
definition: A portal where either the aggregated resources are restricted to those describing or associated with the community or access to the portal is limited to the members of the community.
subclass of: Portal
created date: September 10, 2009

Rendering software
type: Class
definition: A resource that provides an application or program that is used to generate an image from a model, where the model describes three-dimensional objects in a strictly defined language or data structure. In the graphics pipeline, it is the last major step, giving the final appearance to the models and animation.
subclass of: Data visualization software
created date: September 10, 2009

Software library
type: Class
definition: A resource that provides a collection of subroutines or classes used to develop software. Software libraries contain code and data that provide services to independent programs. This allows code and data to be shared and changed in a modular fashion.
subclass of: Software toolkit
created date: September 10, 2009

Electrical recording assay
type: Class
synonym: Electrical recording
subclass of: birnlex_11025
created date: September 23, 2008
contributor: Maryann Martone

Micro-electrode recording assay
type: Class
synonym: micro-electrode recording
synonym: Microelectrode recording
subclass of: Electrical recording assay
created date: September 23, 2008

Intracellular electrode recording assay
type: Class
synonym: Intracellular electrode recording
subclass of: Micro-electrode recording assay
created date: September 23, 2008
contributor: Maryann Martone

Intrathecal
type: Class
definition: Inside the spinal canal (the canal in successive vertebrae through which the spinal cord passes-Wordnet definition) . For example, intrathecal immunoglobulin production means production of this substance in the spinal cord; intrathecal injection is an injection into the the spinal canal (intrathecal space surrounding the spinal cord), as in a spinal anaesthesia or in chemotherapy or pain management applications.
subclass of: BFO_0000028
created date: September 23, 2009
contributor: Maryann Martone

Magnetic resonance imaging
type: Class
synonym: magnetic resonance imaging assay
synonym: MRI
synonym: MRI assay
synonym: MRI imaging
subclass of: birnlex_11026
subclass of: Restriction
  on property: BFO_0000055
  some values from: Neuroimaging role
created date: September 23, 2008
contributor: Maryann Martone

Diffusion magnetic resonance imaging
type: Class
definition: A magnetic resonance imaging (MRI) method that produces in vivo images of biological tissues weighted with the local microstructural characteristics of water diffusion. The field of diffusion MRI can be understood in terms of two distinct classes of application – Diffusion Weighted MRI and Diffusion Tensor MRI. (Adapted from wikipedia: http://en.wikipedia.org/wiki/Diffusion_MRI)
subclass of: Magnetic resonance imaging
created date: September 24, 2009
contributor: Maryann Martone

Functional MRI assay
type: Class
synonym: fMRI
synonym: functional magnetic resonance imaging
synonym: functional magnetic resonance imaging assay
subclass of: Magnetic resonance imaging
created date: September 23, 2009
contributor: Maryann Martone

Diffusion tensor imaging assay
type: Class
synonym: Diffusion tensor imaging
synonym: DTI
abbrev: DTI
subclass of: Diffusion magnetic resonance imaging
created date: September 23, 2008
contributor: Maryann Martone

Diffusion weighted magnetic resonance imaging assay
type: Class
synonym: Diffusion weighted imaging
subclass of: Diffusion magnetic resonance imaging
created date: September 23, 2008
contributor: Maryann Martone

High angular resolution diffusion imaging
type: Class
abbrev: HARDI
subclass of: Diffusion magnetic resonance imaging
created date: September 23, 2008
contributor: Maryann Martone
defining citation: Tuch DS, Reese TG, Wiegell MR, et al (2002). "High angular resolution diffusion imaging reveals intravoxel white matter fiber heterogeneity". Magn. Res. Med. 48: 577–582
PMID: 12353272

Magnetoencephalography
type: Class
synonym: MEG
definition: Magnetoencephalography is an imaging technique used to measure the magnetic fields produced by electrical activity in the brain via extremely sensitive devices such as superconducting quantum interference devices (SQUIDs). These measurements are commonly used in both research and clinical settings. There are many uses for the MEG, including assisting surgeons in localizing a pathology, assisting researchers in determining the function of various parts of the brain, neurofeedback, and others. - definition adapted from Wikipedia
subclass of: birnlex_11026
subclass of: Restriction
  on property: BFO_0000055
  some values from: Neuroimaging role
created date: September 25, 2009
contributor: Maryann Martone

Tract tracing assay
type: Class
synonym: axonal tract tracing
definition: An assay in which a tracer is injected into a region of the nervous system or one of its targets that is taken up by cells, axons or axon terminals in order to determine axonal projections to or from that region.
subclass of: birnlex_11025
created date: September 24, 2009

Tracing role
type: Class
definition: A molecule that is used to trace axonal projections either to or from a part of the nervous system or one of its targets.
subclass of: birnlex_11019
version info: 87157
created date: December 10, 2010
contributor: Maryann Martone

Anterograde tracing role
type: Class
definition: Role of a substance that is used for tract tracing studies in the nervous system that is taken up by cell bodies and transported towards the axon terminals.
subclass of: Tracing role
disjoint with: Post mortem tract tracing role
disjoint with: Retrograde tracing role
disjoint with: Transneuronal tracing role
version info: 134498
created date: December 10, 2010
contributor: Maryann Martone

Post mortem tract tracing role
type: Class
definition: Role of a tracer that can be used to trace connections in post-mortem tissue.
subclass of: Tracing role
disjoint with: Retrograde tracing role
disjoint with: Transneuronal tracing role
version info: 135074
created date: December 10, 2010
contributor: Maryann Martone

Retrograde tracing role
type: Class
definition: Role of a substance that is used for tract tracing studies in the nervous system that is taken up by the axon terminals and transported towards the cell soma.
subclass of: Tracing role
disjoint with: Transneuronal tracing role
version info: 134500
created date: December 10, 2010
contributor: Maryann Martone

Transneuronal tracing role
type: Class
definition: Role of a tracer where the tracer can pass from neuron to neuron through synaptic connections
subclass of: Tracing role
version info: 134529
created date: December 10, 2010
contributor: Maryann Martone

Immunolabeling role
type: Class
subclass of: BFO_0000023
created date: October 20, 2012

Neuroimaging role
type: Class
subclass of: BFO_0000023
created date: October 20, 2012

Longitudinal study design
type: Class
definition: A longitudinal study is a correlational research study that involves repeated observations of the same items over long periods of time. (Adapted from Wikipedia)
subclass of: birnlex_11008
created date: December 23, 2008
contributor: Maryann Martone

Long term potentiation
type: Class
synonym: Long lasting potentiation
synonym: Long term facilitation
synonym: Long-term potentiation
abbrev: LTP
definition: The strengthening (or potentiation) of the connection between two nerve cells which lasts for an extended period of time (minutes to hours in vitro and hours to days and months in vivo). LTP can be induced experimentally by applying a sequence of short, high-frequency stimulations to nerve cell synapses.
subclass of: birnlex_11008
comment: Gene Ontology Biological Process lists Long Term Potentiation etc. I think we should probably just use the GO for now and extend it for neuroscience.
created date: December 23, 2008
contributor: Maryann Martone
defining citation URI: http://www.bio-medicine.org/biology-definition/Long-term_potentiation/

Long term depression
type: Class
abbrev: LTD
subclass of: Long term potentiation
created date: December 23, 2008
contributor: Maryann Martone

Filtered R-weighted back projection
type: Class
subclass of: R-weighted back projection
created date: December 27, 2008
contributor: Maryann Martone
external source id: NITRC_420

Unfiltered R-weighted back projection
type: Class
subclass of: R-weighted back projection
created date: December 27, 2008
contributor: Maryann Martone
external source id: NITRC_421

Reaction time test
type: Class
definition: A behavioral protocol in which response times are assessed.
subclass of: Behavioral paradigm
note: Concept source =mtd
created date: February 4, 2009
has birnlex curator: Jessica Turner

Resting state scan
type: Class
definition: A behavioral paradigm in which the subject rests quietly.
subclass of: Behavioral paradigm
note: Concept source =mtd
created date: February 4, 2009
has birnlex curator: Jessica Turner

Sensory motor task scan
type: Class
definition: A behavioral paradigm in which subjects are asked to press a button each time a checkerboard display flashes. In this blocked design, a flashing checkerboard was displayed for 12 seconds and alternated with 12 second blocks of a fixation cross.
subclass of: Behavioral paradigm
note: Concept source =mtd
created date: February 4, 2009
has birnlex curator: Jessica Turner

B0 field map
type: Class
definition: A gradient-recalled echo pulse sequence that is used to map the geometric distortions caused by static magnetic field inhomogeneities.
subclass of: Echo planar imaging protocol
subclass of: Class
  union of: Magnitude images from a B0 field map
  union of: Phase images from a B0 field map
created date: February 4, 2009
has birnlex curator: Jessica Turner

Instructions to subject
type: Class
synonym: Instruction
definition: The educational process of instructing (research subjects). (MSH); educational process of instructing (research subjects). (CSP)
subclass of: Experimental paradigm
note: Concept Source = UMLS
created date: February 4, 2009
has birnlex curator: Jessica Turner

Localizer scan
type: Class
definition: A localizer scan is one used to determine where the imaging slices should be placed to image the anatomical structures of interest.
subclass of: MRI protocol
created date: February 4, 2009
has birnlex curator: Jessica Turner

Dummy visit protocol
type: Class
definition: MRI Imaging protocol in which data may or may not be collected but are not included in later analyses.
subclass of: MRI protocol
created date: February 4, 2009
has birnlex curator: Jessica Turner

MRI imaging protocol attribute
type: Class
definition: A parameter for an MRI imaging protocol. The value is usually set at the time of scanning/data collection.
subclass of: birnlex_11003
created date: February 4, 2009
has birnlex curator: Jessica Turner

Magnitude images from a B0 field map
type: Class
synonym: Magnitude image from a B0 field mapping protocol
definition: The magnitude images created by a B0 field mapping scan.
subclass of: B0 field map
note: Concept Source = kgh
created date: February 4, 2009
has birnlex curator: Jessica Turner

Phase images from a B0 field map
type: Class
synonym: Phase image from a B0 field mapping protocol
definition: The phase images created by a B0 field mapping scan.
subclass of: B0 field map
note: Concept Source = kgh
created date: February 4, 2009
has birnlex curator: Jessica Turner

Sagittal localizer scan
type: Class
definition: A localizer scan which has a sagittal orientation.
subclass of: Localizer scan
note: Concept Source = kgh
created date: February 4, 2009

Acceleration factors
type: Class
definition: In parallel MRI, the scan time is reduced by increasing the distance in k-space between each phase encoding line by a factor, R, called the acceleration factor.
subclass of: MRI imaging protocol attribute
note: Concept Source = kgh
created date: February 4, 2009

Bandwidth
type: Class
definition: An MR acquisition parameter that defines the range of frequencies that the MR acquisition is sensitive to.
subclass of: MRI imaging protocol attribute
note: Concept Source = kgh
created date: February 4, 2009

MRI coil
type: Class
definition: The type of head and or body coil used for the transmission and reception of radio frequency data in Magnetic Resonance (MR) scanners.
subclass of: MRI imaging protocol attribute
created date: February 4, 2009
external source id: RADLEX ID: RID10813
has birnlex curator: Jessica Turner

Field of view
type: Class
preferred label: Field of View
definition: The total extent of an image along a spatial dimension (Huettel, Song, McCarthy, 2004)
subclass of: MRI imaging protocol attribute
note: Concept Source = mtd
created date: February 4, 2009

Field strength
type: Class
preferred label: Field Strength
definition: The strength of the main magnetic field generated by a magnetic resonance scanner.
subclass of: MRI imaging protocol attribute
note: Concept Source = kgh
created date: February 4, 2009

Flip angle
type: Class
preferred label: Flip Angle
definition: The change in the precession angle of the net magnetization following excitation (Huettel, Song, McCarthy, 2004).
subclass of: MRI imaging protocol attribute
note: Concept Source = mtd
created date: February 4, 2009

Gap between slices (slice gap)
type: Class
definition: The amount of space between slices of excitation, collected during magnetic resonance scanning.
subclass of: MRI imaging protocol attribute
note: Concept source =mtd
created date: February 4, 2009

Scanner vendor
type: Class
definition: The company who manufactures and distributes the magnetic resonance scanner.
subclass of: MRI imaging protocol attribute
note: Concept source =mtd
created date: February 4, 2009

Gradient strength
type: Class
definition: The maximum magnetic field gradient strength attainable by a set of gradient coils in a magnetic resonance scanner.
subclass of: MRI imaging protocol attribute
note: Concept source = kgh
created date: February 4, 2009

Image orientation
type: Class
definition: The manner in which an image is displayed. When applied to magnetic resonance images, it can be in reference to an anatomical landmark (e.g., parallel to the anterior and posterior commissures) or in reference to inferior-superior, anterior-posterior, or left-right dimensions.sagittal, axial or coronal directions.
subclass of: MRI imaging protocol attribute
note: Concept source =mtd
created date: February 4, 2009

K-space trajectory type
type: Class
synonym: k-space traversal
definition: The path taken through k-space by a given pulse sequence. Different pulse sequences adopt different k-space traversals or trajectories; e.g. 'spiral', 'rectilinear' (Huettel, Song, McCarthy, 2004, modified kgh).
subclass of: MRI imaging protocol attribute
note: Concept source =mtd
version info: TODO:
created date: February 4, 2009
external source id: RadLex ID: RID10757

Matrix
type: Class
definition: The dimensions of the array in computer memory used to store the data acquired during a pulse sequence. Related to the number of phase-encoding steps, frequency-encoding points and number of slices.
subclass of: MRI imaging protocol attribute
note: Concept source =mtd
created date: February 4, 2009

Number of dummy acquisitionsd
type: Class
preferred label: Number of Dummy Acquisitions
definition: The number of images collected at the beginning of a functional run that are discarded, usually without examination. This is done because the change in net magnetization following excitation has not yet reached a steady state. (Huettel, Song, & McCarthy, 2004)
subclass of: MRI imaging protocol attribute
note: Concept source =mtd
created date: February 4, 2009

Number of Slices
type: Class
definition: The number of slices collected during an MRI experiment. A slice is a single slab of an imaging volume. (Huettel, Song, McCarthy, 2004).
subclass of: MRI imaging protocol attribute
note: Concept source =mtd
created date: February 4, 2009

Number of time points
type: Class
definition: The number of fMRI images collected at different points in time. Usually used in reference to a single run of an experiment. Each time point is equal to a single TR (repetition time) interval.
subclass of: MRI imaging protocol attribute
note: Concept source =mtd
created date: February 4, 2009

Phase direction
type: Class
definition: The direction in which phase is encoded. Typically discussed in conjunction with frequency encoding. The combination of the two allow for spatial localization within a slice.
subclass of: MRI imaging protocol attribute
note: Concept source =mtd
created date: February 4, 2009
has birnlex curator: Jessica Turner

Read direction
type: Class
synonym: readout direction
definition: The direction in which the frequency encoding gradient is applied. Also called the 'readout' direction.
subclass of: MRI imaging protocol attribute
note: Concept source =mtd
created date: February 4, 2009
has birnlex curator: Jessica Turner

Scanner model
type: Class
definition: The name given to a certain magnetic resonance scanner hardware configuration. For example, one GE model is the 3.0T Signa Excite HD.
subclass of: MRI imaging protocol attribute
note: Concept source = mtd, kgh
created date: February 4, 2009
has birnlex curator: Jessica Turner

Scanner operating system
type: Class
definition: The version of software that controls the operation of a computer and directs the processing of programs (as by assigning storage space in memory and controlling input and output functions) on a magnetic resonance scanner. (adapted from www.m-w.com)
subclass of: MRI imaging protocol attribute
note: Concept source =mtd
created date: February 4, 2009
has birnlex curator: Jessica Turner

Slew rate
type: Class
definition: The maximum rate of change of signal; usually refers to the current supplied to the magnetic field gradient coils.
subclass of: MRI imaging protocol attribute
note: Concept source = kgh
created date: February 4, 2009
has birnlex curator: Jessica Turner

Slice order
type: Class
definition: The order in which slices, slabs of an imaging volume are acquired. Two typical methods are sequential and interleaved. Sequential collection involves collecting slices in adjacent order, or in adjacent order with a small gap between slices (e.g., 1,2,3,4,5,6). Interleaved collection involves collecting every other slice, and then taking a second pass to collect the others (e.g., 1,3,5,2,4,6). Slices can be collected along any of the planes (e.g., inferior to superior, left to right, posterior to anterior).
subclass of: MRI imaging protocol attribute
note: Concept source = mtd
created date: February 4, 2009

Slice thickness
type: Class
definition: The thickness of the slabs of an imaging volume. Typically measured in units of millimeters. A single slice is defined by the the strength of the gradient and the bandwidth of the electromagnetic pulse used to select it. (Huettel, Song, & McCarthy, 2004).
subclass of: MRI imaging protocol attribute
note: Concept source = mtd
created date: February 4, 2009
has birnlex curator: Jessica Turner

With online motion correction
type: Class
definition: Refers to the usage of a pulse sequence, applied before any other data is acquired, that registers the subsequent imaging volume to an imaging volume acquired at an earlier time.
subclass of: MRI imaging protocol attribute
note: Concept source = kgh
created date: February 4, 2009
has birnlex curator: Jessica Turner

Image description and protocol name
type: Class
synonym: Protocol
definition: A protocol is a rule which guides how an activity should be performed; a set of formal rules used to specify the format of an exchange of data. (NCI)
subclass of: MRI imaging protocol attribute
note: Concept source = UMLS
created date: February 4, 2009
has birnlex curator: Jessica Turner

Image description and standard sequence name
type: Class
definition: Non-manufacturer specific name for an imaging protocol, e.g. 'echo-planar imaging' rather than 'ep2d'.
subclass of: MRI imaging protocol attribute
note: Concept source = kgh
created date: February 4, 2009
has birnlex curator: Jessica Turner

3D T1 Weighted Scan
type: Class
definition: A T1 Weighted scan which is acquired as a volume rather than slice by slice.
subclass of: T1 weighted protocol
note: Concept Source = kgh
created date: February 4, 2009
has birnlex curator: Jessica Turner

Defaced T1 scan
type: Class
definition: This refers to a T1 image that has undergone a post-processing technique to remove identifiable facial features.
subclass of: T1 weighted protocol
note: Concept Source = mtd
created date: February 4, 2009
has birnlex curator: Jessica Turner

Diffusion weighted direction set name
type: Class
definition: Common or vendor name and number of diffusion-weighted directions (i.e., Jones30, Siemens default 30, …)
subclass of: DTI imaging protocol attribute
version info: TODO:
created date: February 9, 2009
has birnlex curator: Karl Helmer

DTI imaging protocol attribute
type: Class
subclass of: birnlex_11003
created date: February 9, 2009
has birnlex curator: Karl Helmer

Total number of b-values / volume
type: Class
definition: The number of b=0 volumes plus the number of b NE 0 volumes.
subclass of: DTI imaging protocol attribute
created date: February 9, 2009
has birnlex curator: Karl Helmer

b value(s)
type: Class
definition: The list of diffusion-weighting gradient amplitude vectors
subclass of: DTI imaging protocol attribute
created date: February 9, 2009
has birnlex curator: Karl Helmer

Diffusion-weighted imaging protocol
type: Class
definition: A magnetic resonance imaging protocol that is sensitive to the diffusion of water molecules.
subclass of: Structural MRI protocol
created date: February 9, 2009
external source id: UMLS, C1136216

Eigenvector
type: Class
definition: Vector quantities obtained by diagonalizing the diffusion tensor
subclass of: Vector
created date: February 9, 2009
contributor: Karl Helmer

Anisotropy characteristic value
type: Class
subclass of: birnlex_11004
created date: February 9, 2009
contributor: Karl Helmer
has birnlex curator: Karl Helmer

Fractional anisotropy
type: Class
abbrev: FA
definition: Scalar quantity used to characterize diffusional anisotropy
subclass of: Anisotropy characteristic value
created date: February 9, 2009
contributor: Karl Helmer
has birnlex curator: Karl Helmer

Relative anisotropy
type: Class
abbrev: RA
definition: Scalar quantity used to characterize diffusional anisotropy
subclass of: Anisotropy characteristic value
created date: February 9, 2009
contributor: Karl Helmer
has birnlex curator: Karl Helmer

Eigenvalue
type: Class
definition: scalar quantities obtained by diagonalizing the diffusion tensor
subclass of: Anisotropy characteristic value
created date: February 9, 2009
contributor: Karl Helmer
has birnlex curator: Karl Helmer

Journal
type: Class
definition: A periodical or magazine, esp. one published for a special group, learned society, or profession: the Journal of Neuroscience.
subclass of: birnlex_11038
created date: April 2, 2009

Image registration
type: Class
definition: Data transformation where different sets of images are aligned to a single coordinate system.
subclass of: birnlex_11024
editorial note: I looked at OBI and could not tell from their current classes where this set of entities should go. So I'm putting it here temporarily. (Maryann Martone)
created date: April 23, 2009

Rigid image registration
type: Class
subclass of: Image registration
created date: April 23, 2009

Electronic laboratory notebook
type: Class
synonym: Electronic lab notebook
abbrev: ELN
definition: An electronic lab notebook is a software program designed to replace paper laboratory notebooks (adapted from Wikipedia).
subclass of: birnlex_11012
created date: April 24, 2009
contributor: Maryann Martone

Data role
type: Class
subclass of: BFO_0000023
created date: April 24, 2009

Benchmarking dataset
type: Class
definition: Benchmarking is the process of comparing the cost, cycle time, productivity, or quality of a specific process or method to another that is widely considered to be an industry standard or best practice.
subclass of: Data role

Genome-wide association study
type: Class
abbrev: GWAS
definition: A type of study that examines genetic variation across a given genome, designed to identify genetic associations with observable traits. In human studies, this might include traits such as blood pressure or weight, or why some people get a disease or condition. (Adapted from Wikipedia)
subclass of: birnlex_11010
created date: April 30, 2009
has curation status: graph position temporary

Electromyography surface recording protocol
type: Class
synonym: Electromyography
definition: A macro-electrode recording technique for recording the activation signal of muscles through the use of surface electrode. EMG may also be performed intramuscularly by inserting a needle into the muscle (intramuscular EMG)
subclass of: Micro-electrode recording protocol
created date: May 15, 2009
contributor: Maryann Martone
acronym: EMG

Fear conditioning paradigm
type: Class
definition: Classical conditioning paradigm where a painful or otherwise aversive stimulus is paired with a neutral stimulus leading to the neutral stimulus provoking a state of fear.
subclass of: Classical conditioning paradigm
created date: May 19, 2009
contributor: Maryann Martone

Chromagen
type: Class
definition: A substance giving origin to a coloring matter that is detectable by eye in a chemical reaction.
subclass of: birnlex_11033
created date: June 21, 2009
contributor: Maryann Martone

Fluorescence resonance energy transfer
type: Class
synonym: Förster resonance energy transfer
abbrev: FRET
definition: A type of energy transfer between two fluorophores whereby a donor fluorophore, intially in its electronic excited state, may transfer energy to an acceptor fluorophore (in close proximity, typically <10 nm) through nonradiative dipole-dipole coupling. (adapted from Wikipedia)
subclass of: BFO_0000015

Calcium indicator dye
type: Class
synonym: Calcium dye
definition: Compound that serves to sense changes in calcium levels, usually through a change in fluorescence properties upon binding to calcium.
subclass of: birnlex_11033
created date: June 21, 2009
contributor: Maryann Martone

Biosensor
type: Class
definition: Definition::A device for the detection of an analyte that combines a biological component with a physicochemical detector component. 1) the sensitive biological element (biological material (eg. tissue, microorganisms, organelles, cell receptors, enzymes, antibodies, nucleic acids, etc), a biologically derived material or biomimic) The sensitive elements can be created by biological engineering. 2) the transducer or the detector element (works in a physicochemical way; optical, piezoelectric, electrochemical, etc.) that transforms the signal resulting from the interaction of the analyte with the biological element into another signal (i.e., transducers) that can be more easily measured and quantified; 3) associated electronics or signal processors that is primarily responsible for the display of the results in a user-friendly way.[2] The most widespread example of a commercial biosensor is the blood glucose biosensor, which uses the enzyme glucose oxidase to break blood glucose down. In doing so it first oxidizes glucose and uses two electrons to reduce the FAD (a component of the enzyme) to FADH2. This in turn is oxidized by the electrode (accepting two electrons from the electrode) in a number of steps. The resulting current is a measure of the concentration of glucose. In this case, the electrode is the transducer and the enzyme is the biologically active component. (from Wikipedia
subclass of: birnlex_11033
created date: June 22, 2009
contributor: Maryann Martone

Histochemical protocol
type: Class
synonym: Histochemistry
subclass of: Microscopy contrast enhancement protocol
created date: June 24, 2009
contributor: Maryann Martone

High-pressure liquid chromotography protocol
type: Class
synonym: HPLC protocol
subclass of: birnlex_11010
created date: June 24, 2009
contributor: Maryann Martone

Immunolabeling
type: Class
equivalent class: Class
  intersection of: Staining
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Immunolabeling role
created date: June 24, 2009
contributor: Maryann Martone

Immunocytochemistry
type: Class
subclass of: Staining
subclass of: Restriction
  on property: BFO_0000055
  some values from: Immunolabeling role
created date: June 24, 2009
contributor: Maryann Martone

Immunohistochemistry
type: Class
definition: Immunolabeling protocol application that involves localizing proteins in a tissue section through exploiting the principle of antibodies binding specifically to antigens in biological tissues. It takes its name from the roots "immuno," in reference to antibodies used in the procedure, and "histo," meaning tissue (compare to immunocytochemistry). (from wikipedia)
subclass of: Staining
subclass of: Restriction
  on property: BFO_0000055
  some values from: Immunolabeling role
created date: June 24, 2009
contributor: Maryann Martone

In-situ hybridization
type: Class
synonym: in situ hybridization
abbrev: ISH
subclass of: Specimen preparation
created date: June 24, 2009
contributor: Maryann Martone

National Institute of Alcohol Abuse & Alcoholism
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NIAAA
defining citation URI: http://www.niaaa.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Institute of Aging
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NIA
defining citation URI: http://www.nia.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Institute of Allergy and Infectious Diseases
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NIAID
defining citation URI: http://www.niaid.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Institute of Arthritis and Musculoskeletal and Skin Diseases
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NIAMS
defining citation URI: http://www.niams.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Institute of Biomedical Imaging and Bioengineering
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NIBIB
defining citation URI: http://www.nibib.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Cancer Institute
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NCI
defining citation URI: http://www.nci.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

Center for Disease Control and Prevention
type: United States Department of Health and Human Services granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: CDC
defining citation URI: http://www.cdc.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Institutes of Health Clinical Center
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: CLC
defining citation URI: http://clinicalcenter.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Institute of Child Health and Human Development
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NICHD
defining citation URI: http://www.nichd.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Institute of Deafness and Other Communication Disorder
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NIDCD
defining citation URI: http://www.nidcd.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Institute of Dental and Cranialfacial Research
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NIDCR
defining citation URI: http://www.nidcr.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Institute of Diabetes and Digestive and Kidney Diseases
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NIDDK
defining citation URI: http://www.niddk.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

Office of the Director of the National Institutes of Health
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: OD
defining citation URI: http://www.nih.gov/icd/od/index.htm
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Institute of Drug Abuse
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NIDA
defining citation URI: http://www.nida.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Institute of Environmental Health Sciences
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NIEHS
defining citation URI: http://www.niehs.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Eye Institute
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NEI
defining citation URI: http://www.nei.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

Food and Drug Administration
type: United States Department of Health and Human Services granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: FDA
defining citation URI: http://www.fda.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Institute of General Medical Sciences
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NIGMS
defining citation URI: http://www.nigms.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

Agency for Healthcare Research and Quality
type: United States Department of Health and Human Services granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: AHRQ
defining citation URI: http://www.ahrq.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

Agency for Toxic Substances and Disease Registry
type: United States Department of Health and Human Services granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: ATSDR
defining citation URI: http://www.atsdr.cdc.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

Health Resources and Services Administration
type: United States Department of Health and Human Services granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: HRSA
defining citation URI: http://www.hrsa.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Heart, Lung and Blood Institute
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NHLBI
defining citation URI: http://www.nhlbi.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Human Genome Research Institute
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NHGRI
defining citation URI: http://www.nhgri.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

John E. Fogarty International Center For Advanced Study in the Health Sciences
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: FIC
defining citation URI: http://www.fic.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Library of Medicine
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NLM
defining citation URI: http://www.nlm.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Institute of Mental Health
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NIMH
defining citation URI: http://www.nimh.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Center on Minority Health and Health Disparities
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NCMHD
defining citation URI: http://www.ncmhd.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Institute of Neurological Disorders and Stroke
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NINDS
defining citation URI: http://www.ninds.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Institute of Nursing Research
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NINR
defining citation URI: http://www.ninr.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Center for Complementary and Alternative Medicine
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NCCAM
defining citation URI: http://www.nccam.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

Center for Scientific Review
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: CSR
defining citation URI: http://www.csr.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Center for Research Resources
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: NCRR
defining citation URI: http://www.ncrr.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

Substance Abuse and Mental Health Services Administration
type: United States Department of Health and Human Services granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: SAMHSA
defining citation URI: http://www.samhsa.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

Womens Health Initiative
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: WHI
defining citation URI: http://www.nhlbi.nih.gov/whi/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Institutes of Health Center for Information Technology
type: National Institutes of Health granting agency
type: NamedIndividual
editorial note: Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
created date: 2007-10-14
modified date: 2007-10-14
acronym: CIT
defining citation URI: http://www.cit.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

National Institutes of Health
type: United States Department of Health and Human Services granting agency
type: NamedIndividual
abbrev: NIH
created date: 2007-10-14
modified date: 2007-10-14
defining citation URI: http://www.nih.gov/
has birnlex curator: Bill Bug
has curation status: graph position temporary

FONAR
type: Vendor
type: NamedIndividual
created date: 2008-03-14
modified date: 2008-03-14
defining citation URI: http://www.fonar.com
has birnlex curator: Bill Bug
has curation status: pending final vetting

Hitachi Medical Systems
type: Vendor
type: NamedIndividual
created date: 2008-03-14
modified date: 2008-03-14
defining citation URI: http://www.hitachimed.com
has birnlex curator: Bill Bug
has curation status: pending final vetting

Philips Medical Systems
type: Vendor
type: NamedIndividual
created date: 2008-03-14
modified date: 2008-03-14
defining citation URI: http://www.medical.philips.com
has birnlex curator: Bill Bug
has curation status: pending final vetting

Siemens Medical Solutions
type: Vendor
type: NamedIndividual
created date: 2008-03-14
modified date: 2008-03-14
defining citation URI: http://www.siemensmedical.com
has birnlex curator: Bill Bug
has curation status: pending final vetting

Toshiba Medical Systems
type: Vendor
type: NamedIndividual
created date: 2008-03-14
modified date: 2008-03-14
defining citation URI: http://www.medical.toshiba.com
has birnlex curator: Bill Bug
has curation status: pending final vetting

Varian
type: Vendor
type: NamedIndividual
created date: 2008-03-14
modified date: 2008-03-14
defining citation URI: http://www.varianinc.com
has birnlex curator: Bill Bug
has curation status: pending final vetting

Bruker Biospin MRI
type: Vendor
type: NamedIndividual
created date: 2008-03-14
modified date: 2008-03-14
defining citation URI: http://www.bruker-biospin.com
has birnlex curator: Bill Bug
has curation status: pending final vetting

General Electric Medical Systems
type: Vendor
type: NamedIndividual
synonym: GE Medical Systems
created date: 2007-10-16
modified date: 2008-03-14
defining citation URI: http://www.gemedicalsystems.com
has birnlex curator: Bill Bug
has birnlex curator: Jessica Turner
has curation status: pending final vetting

Cognitive Atlas Concept
comment: Cognitive Atlas Ontology did not have any label or definition for this class. The label is given only for the purpose of grouping the terms. (December 2012)