]> 1.2 NIF-Investigation v.1.2 (July, 2009) - New classes have been added from NeuroLex wiki since the February release (Class ID: nlx_inv_20090401 to 20090610). v2.0 (August 15, 2011): NIF-Investigation now imports NIF-Resource.owl, NIF-Government-Granting-Agency.owl, and NIF-Scientific-discipline.owl as part of its direct imports. Anatomical entity This class is native to NIF-Gross Anatomy, and therfore will have its annotations fine once loaded with NIF-Gross anatomy. The children of this class will be handled when the OBI-Proxy classes are fixed. Mass spectrometry assay 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. Mass spec Mass spectrometry September 24, 2009 mass spectroscopy Immunoprecipitation assay An assay by which an antigen is precipitated from solution using an antibody. Immunoprecipitation Maryann Martone OBI has immunoprecipitation under "process"; we insert "assay" in between process and immunoprecipitation. Not sure what to do here. September 24, 2009 Chromatin immunoprecipitation assay 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. Chromatin immunoprecipitation February 12, 2010 Ontology for BIomedical Investigation Vendor 2007-10-16 2007-10-16 Vendor http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting R-weighted back projection 2006-06-01 2006-10-11 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. 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. BF_T0000139 R-weighted back projection http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Normal control group 2006-06-01 2007-03-05 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. BF_T0000217 Normal control group http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlexInvestigation_174 Structural MRI platform 2006-06-01 2006-10-11 MRI platform Structural MRI platform http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Action observation paradigm 2006-06-01 2006-10-11 A behavioral paradigm in which subjects view images of moving body parts (Brain Map). Action Observation Action observation paradigm BF_T0000338 Clarify the exact nature of this task http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BrainMap.org http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting Sample sectioning 2006-06-01 2006-10-11 Sample sectioning http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Episodic recall paradigm 2006-06-01 2006-10-11 A behavioral paradigm in which subjects recall items from episodic memory (autobiographical history, long-term event memories). Episodic recall paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Angie_Laird http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BrainMap.org http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Difference 2007-03-09 2007-03-09 A quantitative value representing the difference of two underlying quantitative values. Difference http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Breathhold paradigm 2006-06-01 2006-10-11 A behavioral paradigm that requires subjects to hold their breath one or more times. BF_T0000271 Breathhold paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Angie_Laird http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BrainMap.org http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#curation_complete TR 2007-03-09 2007-03-09 February 9, 2009 MRI repetition time Repetition time TODO: TR 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. 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). http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Sham control group 2006-06-01 2006-10-11 A subject group that has received an identical treatment to the experimental group but without the active agent under study. BF_T0000148 Sham control group a placebo-treated control group http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBI-proxy.owl#birnlex_11045 http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlexInvestigation_174 Functional MRI platform 2006-06-01 2006-10-11 Functional MRI platform fMRI platform http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Acupuncture paradigm 2006-06-01 2006-10-11 A behavioral paradigm where subjects are stimulated with Chinese acupuncture, a procedure in which thin needles are passed through the skin to specific points. Acupuncture paradigm BF_T0000339 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Angie_Laird http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BrainMap.org http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary Sample dissection 2006-06-01 2006-10-11 Sample dissection http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Divided auditory attention paradigm 2006-06-01 2006-10-11 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. BF_T0000347 Divided auditory attention paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Angie_Laird http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BrainMap.org http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Encoding paradigm 2006-06-01 2006-10-11 A behavioral paradigm in which a subject views stimuli (words, pictures, letters) and are instructed to memorize them. BF_T0000358 Encoding paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Angie_Laird http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BrainMap.org http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Unit 2007-03-09 2007-03-09 Uniform measurement standard used to characterize a quantitative value. Unit http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Investigator role 2006-07-15 2008-02-21 Investigator role Role played by individual investigators during the course of an investigation http://obi.sourceforge.net/ontology/OBI.owl#OBI_54 http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBI-proxy.owl#birnlex_11015 Classical conditioning paradigm 2006-06-01 2006-10-11 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. BF_T0000343 Classical conditioning paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Angie_Laird http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BrainMap.org http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Assessment * 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) 2006-06-01 2006-10-11 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. Assessment BF_T0000276 C0039593 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#curation_complete test Tesla 2007-03-09 2007-03-09 T Tesla 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. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Sham operated control group 2006-06-01 2007-08-24 A subject group that has received an identical surgical procedure to the experimental group but without the treatment under study. BF_T0000150 Sham operated control group http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlexInvestigation_174 http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_11046 Cognitive assessment 2006-06-01 2006-10-11 C0870300 Cognitive assessment http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS Talairach-Tournoux Atlas 125100 2007-03-09 2007-03-09 A standardized brain atlas published by Talairach and Tournoux. Talairach-Tournoux Atlas http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Genotype 2006-06-01 2006-10-11 Genotype http://obi.sourceforge.net/ontology/OBI.owl#OBI_3 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#definition_incomplete Serial item recognition paradigm 2006-06-01 2006-10-11 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). BF_T0000219 SIRP Serial item recognition paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated moved under the new Item_recognition_paradigm class (BB). Behavioral assessment 2006-06-01 2006-10-11 Behavioral assessment http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Verbal fluency assessment 2006-06-01 2006-10-11 BF_T0000225 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. Verbal fluency assessment http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Christine_Fennema-Notestine http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting Monoclonal antibody 2006-05-15 2007-03-05 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) BF_T0000034 Monoclonal Monoclonal antibodies Monoclonal antibody http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated mAb 2D spatial image 2007-03-09 2007-03-09 2D spatial image A type of image where pixel values represent a quantity measure over 2 spatial dimensions. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Confocal microscope 2006-05-15 2006-10-11 Confocal microscope http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Neuropsychological assessment 2006-06-01 2006-10-11 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) C0027902 Neuropsychological assessment http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Christine_Fennema-Notestine http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS Sternberg paradigm 2006-06-01 2006-10-11 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). BF_T0000359 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 DMTS Need to clarify what a Sternberg paradigm involves Sternberg paradigm delayed match-to-sample paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Angie_Laird http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BrainMap.org http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting moved under the new Item_recognition_paradigm class (BB). Polyclonal antibody 2006-05-15 2007-03-05 BF_T0000035 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) Polyclonal Polyclonal antibodies Polyclonal antibody http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated polyAb MRI 3D image 2007-03-07 2007-03-07 A type of 3D image collected using an MRI device. MRI 3D image http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Biochemical specimen preparation protocol 2006-06-01 2007-03-05 Biochemical specimen preparation protocol Changed name from the ambiguous Biochemical_protocol to Biochemical_specimen_preparation_protocol (BB). http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug Laser scanning confocal microscope 2006-05-15 2006-10-11 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) BF_T0000022 Laser scanning confocal microscope http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS_defSource Visual oddball paradigm An oddball discrimination paradigm where subjects view letters or objects and indicate when they see a target stimulus. BF_T0000340 Visual oddball paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Angie_Laird http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BrainMap.org http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Contrast agent 2006-05-15 2007-03-05 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) C0009924 Contrast agent Substances used in radiography that allow visualization of certain tissues. (CSP) Substances used in radiography that allow visualization of certain tissues. (MeSH) http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Left handedness 2006-04-04 2006-10-11 A behavioral phenotype where the subject preferentially uses the left hand for tasks requiring the use of a single hand or a dominant hand. C0234418 Left handedness http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS Microscopy contrast enhancement protocol 2006-05-15 2007-03-05 Changed preferred Label from Contrast_enhancement_protocol to Microscopy_contrast_enhancement_protocol. Microscopy contrast enhancement protocol 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). _7_6 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated MRI 2D image 2007-03-07 2007-03-07 A type of 2D image collected using an MRI device. MRI 2D image http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Electron microscope 2006-05-15 2006-10-11 C0262879 Electron microscope http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Ambidextrous 2006-04-04 2006-10-11 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. Ambidextrous C0023114 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS Fixation protocol 2006-05-15 2007-03-05 Fixation protocol Should look to FBbi for content here, hopefully brought into BIRNLex-Main via import. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Scanning electron microscope 2006-05-15 2006-10-11 C0262878 Scanning electron microscope http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Cognitive phenotype 2006-06-01 2006-10-11 Cognitive phenotype http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Immunolabeling protocol 2006-05-15 2007-03-05 Immunolabeling protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Sensorimotor paradigm 2006-06-01 2006-10-11 A behavioral paradigm that requires the subject respond to stimuli that are dissimilar to the majority of stimuli presented BF_T0000266 Sensorimotor paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#curation_complete Transmission electron microscope 2006-05-15 2006-10-11 C0262880 Transmission electron microscope http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#definition_incomplete Intramuscular injection 2006-06-01 2006-10-11 C0021492 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) Intramuscular injection administration of a drug via injection into a muscle. (CSP) http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated i.m. Verbal fluency 2006-06-01 2006-10-11 A cognitive phenotype measuring an individual's facility with producing spoken language. BF_T0000225 Verbal fluency http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Christine_Fennema-Notestine http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#curation_complete Intracellular injection protocol 2006-05-15 2007-03-05 Intracellular injection protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Duration 2007-03-09 2007-03-09 A type of temporal characteristic value where the time measured is that between the occurance of two events. Duration http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Free recall ability 2006-06-01 2007-08-24 Free recall ability http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlexInvestigation_202 true Memory phenotype 2006-06-01 2006-10-11 Memory phenotype http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Staining protocol 2006-05-15 2007-03-05 Staining protocol _7_6.2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Body weight 2006-06-01 2007-08-24 A measure of the mass of the entire body of the organism. Body weight C0005910 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlexInvestigation_204 Subthelial injection 2006-06-01 2006-10-11 Subthelial injection http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Blood Oxygenation Level Dependent signal 2007-03-09 2007-03-09 BOLD Blood Oxygenation Level Dependent signal 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). PMID:1948051 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Collaborator 2006-07-15 2007-03-05 BF_T0000184 Collaborator 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. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Organism attribute 2006-06-01 2007-08-24 Organism attribute What is this and how would it differ from Phenotype_attribute (BB)? http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlexInvestigation_199 true Mild cognitive impairment 2006-06-01 2006-10-11 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. BF_T0000227 Mild cognitive impairment http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Christine_Fennema-Notestine http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated TA 2007-03-09 2007-03-09 MRI acquitision time TA 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) The time the MRI scanner takes to collect an MRI image. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Sham operated role 2006-06-01 2008-02-21 A subject group that has received an identical surgical procedure to the experimental group but without the treatment under study. Sham operated role http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_11018 http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_11046 true Physical phenotype 2006-06-01 2006-10-11 Physical phenotype http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Protein expression phenotype 2006-06-01 2006-10-11 Protein expression phenotype http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Experimental paradigm 2006-06-01 2006-10-11 BF_T0000261 Experimental paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated FMRIB Software Library 2007-03-09 2007-03-09 FMRIB Software Library FSL 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/). http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2190 Project leader 2006-07-15 2007-03-05 BF_T0000183 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. Project leader http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Dynamic causal modeling 2007-03-07 2007-03-07 DCM 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. Dynamic causal modeling http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated TE 2007-03-09 2007-03-09 Echo time MRI echo time TE 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). 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 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Working memory phenotype 2006-06-01 2006-10-11 Working memory phenotype http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Gender phenotype 2006-06-01 2006-10-11 Gender phenotype The observable physical characteristics typical of the male or female of the species. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Organism characteristic 2006-07-15 2007-03-05 Organism characteristic http://obi.sourceforge.net/ontology/OBI.owl#OBI_3 Experimenter 2006-07-15 2007-03-05 Experimenter http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Behavioral paradigm 2006-06-01 2006-10-11 BF_T0000262 Behavioral paradigm 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. 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). http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Angie_Laird http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BrainMap.org http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#definition_incomplete http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary Gene specific probe 2006-05-15 Gene specific probe June 25, 2009 http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBI-proxy.owl#birnlex_11020 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Reagent 2006-05-15 2007-03-05 C0034760 Reagent 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) http://obi.sourceforge.net/ontology/OBI.owl#OBI_258 http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBI-proxy.owl#birnlex_11019 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Polynomial coefficient 2007-03-09 2007-03-09 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. Polynomial coefficient http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated proportionality coefficient proportionality coefficient scaling coefficient AFNI 2007-03-07 2007-03-07 AFNI 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/). http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Vector 2007-03-09 2007-03-09 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. Vector http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Molecular phenotype 2006-06-01 2006-10-11 Molecular phenotype http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Protein specific probe 2006-05-15 Protein specific probe http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBI-proxy.owl#birnlex_11020 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Item recognition paradigm 2006-10-11 2006-10-11 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. Item recognition paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting Algorithm 2006-06-01 2007-03-05 A well defined set of rules that can be expressed using formal mathematical expression and thereby implemented in a computing environment. Algorithm C0002045 http://obi.sourceforge.net/ontology/OBI.owl#OBI_5 http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBI-proxy.owl#birnlex_11009 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Brett_Peterson http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#curation_complete http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS Institution 2006-04-04 2006-10-11 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. Institution 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. 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). http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary Phenotype 2006-06-01 2006-10-11 How does this related to Phenotype_attribute and to PaTO expressions (BB)? Phenotype birnlexMain_7 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Delayed matching to sample paradigm 2006-06-01 2006-10-11 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. BF_T0000346 Delayed matching to sample paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Angie_Laird http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BrainMap.org http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated DNA specific probe 2006-05-15 2007-03-05 DNA specific probe http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Lead institution 2006-04-04 2006-10-11 Lead institution http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary Transmission electron microscopic imaging assay 2006-05-15 2006-10-11 Transmission electron microscopic imaging assay http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Cardinal part of imaging instrument 2006-06-01 2006-10-11 Cardinal part of imaging instrument http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Imaging instrument 2006-05-15 2006-10-11 Imaging instrument http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Behavioral phenotype 2006-06-01 2006-10-11 Behavioral phenotype http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Collaborating institution 2006-04-04 2006-10-11 Collaborating institution http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary RNA specific probe 2006-05-15 2007-03-05 RNA specific probe http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Cardinal part of microscope 2006-06-01 2006-10-11 Cardinal part of microscope http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Magnetic resonance imaging scanner 2006-05-15 2006-10-11 MRI scanner Magnetic resonance imaging scanner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Relaxation time 2007-03-07 2007-03-07 Relaxation time We may want to eventually include the 1/e mathematical definition of relaxation time. a type of temporal characteristic value where the time measured is that required to return to an equilibrium state following a well-defined stimulus. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Smoking behavior 2006-06-01 2006-10-11 Smoking behavior http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Toxin 2006-05-15 2007-03-05 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. C0040549 Toxin http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2103_2 true Trail making test 2006-06-01 2006-10-11 BF_T0000223 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 ...). Trail making test http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Christine_Fennema-Notestine http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#curation_complete Microscope 2006-05-15 2006-10-11 An instrument used to obtain a magnified image of small objects and reveal details of structure not otherwise distinguishable. C0181839 Microscope http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS Staining 2006-06-01 2006-10-11 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. Staining http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated T1 relaxation time 2007-03-07 2007-03-07 February 9, 2009 Spin-lattice relaxation time T1 relaxation time We may want to eventually include the 1/e mathematical definition of relaxation time. 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. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Smoking 2006-06-01 2006-10-11 Behavioral phenotype used to describe an individual who currently smokes tobacco products. C0337664 Smoking http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting Antibody 2006-05-15 2007-03-05 Ab Antibody BF_T0000132 Immunoglobulin that is used as a reagent to localize a signal through an immunological reaction. antibodies antibody used for immunocytochemical protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Mini mental state examination 2006-06-01 2006-10-11 BF_T0000222 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) MMSE Mini mental state examination http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Christine_Fennema-Notestine http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#definition_incomplete Optical microscope 2006-05-15 2006-10-11 Optical microscope http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated ssss Past smoking behavior 2006-06-01 2006-10-11 A behavioral phenotype used to describe an individual who is currently not smoking tobacco products but has at some time in the past. C0337671 Past smoking behavior ex smoking behavior former smoking behavior http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting Anatomical atlas data set 2007-03-07 A type of anatomical data set contains a collection of anatomical maps. ABA C57Bl/6 Adult Mouse Brain Atlas AMA atlas of the body Anatomical atlas data set Atlas Franklin-Paxinos C57Bl/6J Adult Mouse Brain Atlas in stereotaxic coordinates (2001). 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. LONI Minimum Deformation C57Bl/6 Mouse Brain Atlas MNI Atlas March 31, 2009 May have to adapt this definition or alter class to reflect that fact some atlases are collections of data sets. NeuroTerrain C57Bl/6 Adult Mouse Brain Atlas Talairach-Tournoux Atlas Yale atlas of echocardiography _1_1.2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Phalloidin 2006-05-15 2007-03-05 C0031312 Phalloidin 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) http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule.owl#CHEBI_8040 true Multiphoton microscope 2006-05-15 2007-10-11 BF_T0000028 December 23, 2008 Definition Modified (December 23, 2008) Multi-photon microscope Multiphoton microscope 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. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Experiment 2006-04-04 2006-10-11 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) BF_T0000189 Experiment 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). Not sure whether this is the same as study; needs clarification (MM). 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. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting T2 weighted 2D image 2007-03-09 2007-03-09 A type of 2D MRI image collected using an T2 Weighted MRI imaging protocol. T2 weighted 2D image http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Anatomical data set 2007-03-07 2007-03-07 A type of data set describing anatomical objects. Anatomical data set http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Non smoking 2006-06-01 2006-10-11 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. C0337672 Non smoking http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS Digital aggregate entity 2007-03-07 2007-03-07 Digital aggregate entity http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Block design 2007-03-07 2007-03-07 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. Block design Box_car_design http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Specimen preparation protocol 2006-05-15 2007-03-05 C0200363 Specimen preparation protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Agent delivery process 2006-05-15 2006-10-11 Agent delivery process BF_T0000274 The process by which an experimental agent is delivered to an organism or part of organism. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#curation_complete ingestion of toxin injection of drug MNI Atlas 2007-03-09 2007-03-09 A standardized brain atlas developed by the Montreal Neurological Institute. MNI Atlas http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Imaging protocol 2007-03-07 2007-03-07 Imaging protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated fMRI beta 2007-03-09 2007-03-09 BETA fMRI beta http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated 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 2006-06-01 2006-10-11 C0232478 Ingestion http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Convolution 2007-03-07 2007-03-07 A mathematical operation that describes the action of a linear system on a signal. Convolution 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. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Vascular perfusion 2006-06-01 2006-10-11 BF_T0000032 Method of agent delivery where the agent is pumped through the vasculature of the animal. 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). Vascular perfusion http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Immersion 2006-06-02 2006-10-11 A process for delivering an agent to an object of study in which the object is physically submersed in the agent. C0020940 Immersion http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS immersion of a tissue sample into fixative Preparative role 2007-03-05 2007-03-05 A role played by a continuant in an investigational protocol designed to prepare a Biomaterial_entity for experimental manipulation. Preparative role http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary Gene expression phenotype 2006-06-01 2006-10-11 Gene expression phenotype http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated nnnnnn T1 weighted protocol 2007-03-07 An MRI scanning pulse sequence that is used to acquire structural data whose tissue contrast parameter is T1-weighted. 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. February 5, 2009 T1 weighted protocol T1 weighted scan http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated mtd, modified from kgh's other anatomical definitions. Injection 2006-06-01 2006-10-11 C0021485 Injection http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Intracellular injection 2006-06-01 2006-10-11 BF_T0000117 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. Intracellular injection http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Instrument operator 2006-07-15 2007-03-05 Instrument operator http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Fixative 2006-05-15 2006-10-11 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) C0016184 Fixative 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) http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated T2 relaxation time 2007-03-09 2007-03-09 February 9, 2009 Is transverse relaxation time truly a synonym for this entity under all conditions (BB: 2007-03-09)? 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. Spin-spin relaxation time T2 relaxation time 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. Transverse relaxation time We may want to eventually include the 1/e mathematical definition of relaxation time. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Microscopic imaging assay 2006-05-15 2006-10-11 Microscopic imaging assay http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Quantitative organism attribute 2006-06-01 2007-08-24 Changed name to singular from plural to comply with univocity constraint (BB). Quantitative organism attribute http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#definition_incomplete http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlexInvestigation_199 Drawing paradigm 2006-06-01 2006-10-11 A behavioral paradigm in which the subject is asked to draw lines, circles or more complex figures using a pen or stylus. BF_T0000356 Drawing paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Angie_Laird http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BrainMap.org http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Glutaraldehyde fixative 2006-05-15 2007-03-05 A crosslinking fixative. Glutaraldehdye is a pentanedial; 5-carbon saturated chain with a highly reactive aldehyde group on each end (MM). 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) C0017814 Glutaraldehyde fixative 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) This is a placeholder for a ChEBI class (BB: 2007-03-05). glutaral glutardialdehyde http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary pentanedial 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) Intraperotineal injection 2006-06-01 2006-10-11 Intraperotineal injection http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated i.p. T2* relaxation time 2007-03-09 2007-03-09 T-two-star T2* relaxation time 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. We may want to eventually include the 1/e mathematical definition of relaxation time. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Data analyzer 2006-07-15 2007-03-05 Data analyzer http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Light microscopic imaging assay 2006-05-15 2006-10-11 Light microscopic imaging assay http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Phenotype attribute 2006-06-01 2007-08-24 Phenotype attribute 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). http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlexInvestigation_199 Specimen fixation 2006-07-15 2006-07-15 BF_T0000236 Specimen fixation 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) http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#MeSH_defSource Intrathecal injection 2006-06-01 2006-10-11 C0021896 Intrathecal injection http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Tannic acid fixative 2006-05-15 2007-03-05 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). 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) C0039294 Tannic acid fixative This is a placeholder for a ChEBI class (BB: 2007-03-05). http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS Principal investigator 2006-07-15 2007-03-05 BF_T0000157 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 Principal investigator http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Electron microscopic imaging assay 2006-05-15 2006-10-11 Electron microscopic imaging assay http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Tissue dissection 2006-05-15 2006-10-11 Tissue dissection http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Paraformaldehyde fixative 2006-05-15 2007-03-05 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). 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) C0070066 Paraformaldehyde fixative This is a placeholder for a ChEBI class (BB: 2007-03-05). http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS Tissue sectioning 2006-05-15 2006-10-11 Tissue sectioning http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Nicotine use assessment 2006-06-01 2006-10-11 Nicotine use assessment http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Energy filter 2006-06-01 2006-10-11 Energy filter http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Fagerstrom test for nicotine dependence 2006-06-01 2006-10-11 C0451156 Fagerstrom test for nicotine dependence http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated is an assessment which consists of a questionnaire that measures nicotine use (Fagerstrom citation) Gross dissection 2006-05-15 2006-10-11 Gross dissection http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Auditory oddball paradigm 2006-06-01 2006-10-11 An oddball discrimination paradigm that involves responding to auditory stimuli that are dissimilar to the majority of auditory stimuli presented. Auditory oddball paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#curation_complete California Verbal Learning Test 2006-06-01 2006-10-11 BF_T0000220 California Verbal Learning Test http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#definition_incomplete Microdissection 2006-05-15 2006-10-11 C0598304 Microdissection http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated In column energy filter 2006-06-01 2006-10-11 In column energy filter http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated 3D spatial image 2007-03-09 2007-03-09 3D spatial image A type of image where pixel values represent a quantity measure over 3 spatial dimensions. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Simple saccade paradigm 2006-06-01 2006-10-11 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) Simple saccade paradigm This term is equivalent to "saccade paradigm" in Brain Map http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Angie_Laird http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BrainMap.org http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting Never has smoked 2006-06-01 2006-10-11 Behavioral phenotype used to describe an individual who has never smoked tobacco products. Never has smoked http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Laser capture 2006-05-15 2006-10-11 C1113652 Laser capture http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated 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) Tissue section 2006-05-15 2006-10-11 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. BF_T0000134 Tissue section http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated T1 weighted 2D image 2007-03-09 2007-03-09 A type of 2D MRI image collected using an T1 Weighted MRI imaging protocol. T1 weighted 2D image http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated PET imaging protocol * 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) 2007-03-07 2007-03-07 An imaging protocol where images are acquired using a Positron Emission Tomography device. C0032743 PET imaging protocol Positron Emission Tomography imaging protocol _7_2.3 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS_defSource Behavioral laterality 2006-04-04 2006-10-11 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) Behavioral laterality C0023114 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. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jeff_Grethe http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS Anti saccade paradigm 2006-06-01 2006-10-11 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) Anti saccade paradigm Anti-saccades paradigm BF_T0000341 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Angie_Laird http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BrainMap.org http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Algorithm execution 2006-06-01 2006-10-11 A transformation that applies an algorithm with specified parameters on a data set on a specific computing platform. Algorithm execution http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jeff_Grethe http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#curation_complete Temporal characteristic value 2007-03-07 2007-03-07 Temporal characteristic value a type of quantitative value measured in units of time. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Oddball discrimination paradigm 2006-06-01 2006-10-11 A behavioral paradigm that assesses a response to non-attended stimuli which are dissimilar to the majority of stimuli presented BF_T0000267 Oddball discrimination paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#curation_complete MRI protocol * 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) 2007-03-07 2008-05-01 An imaging protocol where images are acquired using a Magnetic Resonance Imaging device. C0024485 MRI MRI protocol _7_2.2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS_defSource Handedness 2006-04-04 2006-10-11 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) BF_T0000316 Handedness http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS Covert visual reading paradigm 2006-06-01 2006-10-11 Covert visual reading paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Specimen preparation 2006-06-01 2006-10-11 Specimen preparation http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Mismatch negativity paradigm 2006-06-01 2006-10-11 BF_T0000265 Mismatch negativity paradigm behavioral paradigm that assesses a response to non-attended stimuli which are dissimilar to the majority of stimuli presented. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Intermediate voltage electron microscope 2006-05-15 2006-10-11 BF_T0000030 Intermediate voltage electron microscope Transmission electron microscope cabable of operating at an accelerating voltage in the range of 300-400 KeV http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Longitudinal magnetization 2007-03-09 2007-03-09 Longitudinal magnetization 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 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Right handedness 2006-04-04 2006-10-11 A behavioral phenotype where the subject preferentially uses the right hand for tasks requiring the use of a single hand or a dominant hand. C0234417 Right handedness http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS Covert braille reading paradigm 2006-06-01 2006-10-11 A behavioral paradigm in which a subject reads aloud with fingers. BF_T0000341 Brain Map lists only a Braille reading paradigm but BIRNLex is dividing this into overt and covert Braille reading paradigms Covert braille reading paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Angie_Laird http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BrainMap.org http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting Image reconstruction software 2006-06-01 2006-10-11 Image reconstruction software http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated High voltage electron microscope 2006-05-15 2006-10-11 BF_T0000029 High voltage electron microscope http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated transmission electron microscope cabable of operating an accelerating voltage in the range of 500- 1000 KeV Deductive reasoning paradigm 2006-06-01 2006-10-11 A behavioral paradigm in which subjects are required to utilize problem-solving skills and logic to determine the correct solution; feedback is sometimes given. BF_T0000345 Deductive reasoning paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Angie_Laird http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BrainMap.org http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Longitudinal relaxation time 2007-03-09 2007-03-09 Longitudinal relaxation time We may want to eventually include the 1/e mathematical definition of relaxation time. 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. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Software toolkit 2007-03-07 2007-03-07 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). Software toolkit http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Image processing software 2006-06-01 2006-10-11 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. Image processing software http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Ultrahigh voltage electron microscope 2006-05-15 BF_T0000031 March 31, 2009 Transmission electron microscope capable of operating at an accelerating voltage of > 1 MeV UHVEM Ultrahigh voltage electron microscope http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated T2 weighted protocol 2007-03-07 An MRI scanning pulse sequence that is used to acquire structural data whose tissue contrast parameter is T2-weighted. An imaging protocol typically using longer TE and TR times whose contrast and brightness are predominately determined by T2 signals (2007-03-07) February 5, 2009 T2 weighted protocol T2 weighted scan http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Eye Saccade paradigm 2006-06-01 2006-10-11 A behavioral paradigm in which a subject makes a rapid eye movement relative to an initial target (JB). BF_T0000360 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. Eye Saccade paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BrainMap.org http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jyl_Boline http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting Image analysis software 2006-06-01 2006-10-11 Image analysis software Moved as a subclass of Data processing software from Data analysis software. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2211 Electron tomography software 2006-05-15 2006-10-11 Electron tomography software http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Diffusion tensor imaging protocol 2007-03-07 2007-03-07 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) DTI 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). Diffusion tensor imaging protocol February 9, 2009 Moved as a subclass of 'Diffusion-weighted imaging protocol' from 'Structural MRI protocol'. birnlex_2251 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Reading paradigm 2006-06-01 2006-10-11 A behavioral paradigm in which a subject is asked to read either silently (covert) or aloud (overt) BF_T0000361 Reading paradigm This list contains precoordinated terms that will be addressed at a future date. This term does not differentiate between lexical and semantic parsing by the subject http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#pending_final_vetting Co-investigator 2006-07-15 2007-03-05 Co-investigator http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Imaging platform 2006-06-01 2006-10-11 Imaging platform http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Control group 2006-06-01 2007-03-05 C0009932 Control group 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) http://obi.sourceforge.net/ontology/OBI.owl#OBI_176 http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBI-proxy.owl#birnlex_11044 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS true Image reconstruction algorithm 2006-06-01 2006-10-11 Algorithm used to compute a reconstruction from a set of images, e.g., R-weighted back projection. BF_T0000131 Image reconstruction algorithm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Maryann_Martone http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#curation_complete Eating paradigm 2006-06-01 2006-10-11 BF_T0000357 Behavioral paradigm in which the subject ingests food. Eating paradigm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Angie_Laird http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BrainMap.org http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Magnetic resonance imaging platform 2006-06-01 2006-10-11 Magnetic resonance imaging platform http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Echo planar imaging protocol 2007-03-07 2007-03-07 EPI 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. Echo planar imaging protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Transverse magnetization 2007-03-09 2007-03-09 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*. Transverse magnetization http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Relational database 2007-10-09 A normalized data set constructed according to a specific entity-relation data model. 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) March 31, 2009 Relational database _1_1.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBI-proxy.owl#birnlex_11006 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated true Data acquisition software 2007-10-09 90413 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. Data acquisition software June 12, 2011 _1_2.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Documentation generation software 2007-10-09 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. Documentation generation software June 11, 2011 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Data processing software 2007-10-09 2007-10-09 Data processing software _1_2.2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Data analysis software 2007-10-09 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. Data analysis software June 12, 2011 _4_14 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Image acquisition software 2007-10-09 2007-10-09 Image acquisition software http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Data visualization software 2007-10-09 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. Data visualization software September 10, 2009 _1_2.3 _7_18 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Sequence analysis software 1D correlative analysis software 2007-10-09 2007-10-09 Sequence analysis software _1_2.2.3 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated sequence pattern analysis software Time-series analysis software 2007-10-09 2007-10-09 Time-series analysis software http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated 1D Time-series analysis software 1D Time-series analysis software 2007-10-09 2007-10-09 _1_2.2.2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated 2D Time-series analysis software 2007-10-09 2007-10-09 2D Time-series analysis software http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated 3D Time-series analysis software 2007-10-09 2007-10-09 3D Time-series analysis software 4D analysis software http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Network analysis software 2007-10-09 2007-10-09 Network analysis software _1_2.2.4 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated pathway analysis software 3D visualization software 2007-10-09 2007-10-09 3D visualization software _1_2.3.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated 4D visualization software 2007-10-09 2007-10-09 4D visualization software _1_2.3.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Software development tool 2007-03-07 2007-03-07 Software development tool http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Data compression software 2007-10-09 2007-10-09 Data compression software http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Software development environment 145595 2007-03-07 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. IDE Integrated Software development environment June 11, 2011 Software development environment http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Compiler 2007-03-07 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. Compiler June 11, 2011 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Code Profiler 2007-03-07 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. Code Profiler June 11, 2011 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Code testing framework 2007-03-07 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. Code testing framework June 11, 2011 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Segmentation software 2007-10-09 A tool or resource that comprises computer software functionality, including self-contained executable, software development support or libraries that are invoked by the user on local machines or remote servers (NITRC). April 1, 2009 December 15, 2008 NITRC NITRC NITRC_ID: 333 Segmentation software http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Image alignment software 2007-10-09 388 Added: synonyms, definition and new label. (April 2, 2009) Alignment software Alignment software April 2, 2009 April 24, 2009 Software application that performs image spatial transformation for the purposes of image 'Registration'. (NITRC) This class has been retired http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2195 http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2230 image registration software true Registration software 2007-10-09 2007-10-09 Image Alignment software Registration software http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Data access protocol 2007-10-09 2007-10-09 Data access protocol _2.2_6 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Static HTML document 2007-10-09 2007-10-09 Static HTML document _2.2_1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Dynamic HTML document 2007-10-09 2007-10-09 Dynamic HTML document _2.2_2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Web service 2007-10-09 2007-10-09 90426 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. June 15, 2011 Web service _2.2_4 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Application programming interface 2007-10-09 2007-10-09 API Application programming interface http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated SPECT imaging protocol * 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) 2007-10-09 2007-10-09 C0040399 SPECT imaging protocol Single Photon Emission Computed Tomography imaging protocol _7_2.4 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS_defSource EM imaging protocol 2007-10-09 2007-10-09 EM imaging protocol Electron microscopy imaging protocol _7_4 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated SEM imaging protocol 2007-10-09 2007-10-09 SEM imaging protocol Scanning electron microscopy imaging protocol _7_4.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated TEM imaging protocol 2007-10-09 2007-10-09 TEM imaging protocol Transmission electron microscopy imaging protocol _7_4.2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated STEM imaging protocol 2007-10-09 2007-10-09 STEM imaging protocol Scanning transmission electron microscopy imaging protocol _7_4.3 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Immunohistochemical protocol 2007-10-09 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) IHC Immunohistochemical protocol June 24, 2009 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) _7_6.2.3 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Fluorescence labeling protocol 2007-10-09 2007-10-09 Fluorescence labeling protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Golgi staining protocol 2007-10-09 2007-10-09 Golgi staining protocol _7_6.2.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Immunocytochemistry protocol 2007-10-09 2007-10-09 Immunocytochemistry protocol _7_6.2.2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated network graph visualization software 2007-10-09 2007-10-09 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated network graph visualization software Version source control system (source) code management 2007-03-07 90411 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. June 11, 2011 Revision control Source control Version control (system) Version source control system http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Nissl staining protocol 2007-10-09 2007-10-09 Nissl staining protocol _7_6.2.6 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Myelin staining protocol 2007-10-09 2007-10-09 Myelin staining protocol _7_6.2.4 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Radiolabeling protocol 2007-10-09 2007-10-09 Radiolabeling protocol _7_6.4 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Functional MRI protocol 2007-10-09 2007-10-09 Functional MRI protocol _7_2.2.2 fMRI http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Structural MRI protocol 2007-10-09 2007-10-09 MRI Structural MRI protocol _7_2.2.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Optical imaging protocol 2007-10-09 2007-10-09 Light microscopy imaging protocol Optical imaging protocol _7_7 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Light transmission optical imaging protocol 2007-10-09 2007-10-09 Light transmission optical imaging protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Light emitting optical imaging protocol 2007-10-09 2007-10-09 Light emitting optical imaging protocol _7_7.3 fluorescence/chemiluminescence/phosphorescence optical imaging protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Bright-field imaging protocol 2007-10-09 2008-05-01 Bright-field imaging protocol _7_7.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Dark-field imaging protocol 2007-10-09 2008-05-01 Dark-field imaging protocol _7_7.2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Multiphoton imaging protocol 2007-10-09 Added: definition and synonyms (April 2, 2009) An imaging protocol that produces images using a microscopy in multiphoton mode. April 2, 2009 Multiphoton imaging Multiphoton imaging protocol Multiphoton microscopy _7_7.3.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Confocal imaging protocol 2007-10-09 April 2, 2009 Confocal imaging protocol Synonyms added (April 2, 2009) _7_7.3.2 confocal imaging confocal microscopy http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Laser scanning confocal imaging protocol 2007-10-09 2007-10-09 Laser scanning confocal imaging protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Fluorescence resonance energy transfer imaging protocol 2007-10-09 FRET FRET protocol Fluorescence resonance energy transfer imaging protocol June 23, 2009 _7_7.3.3 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Differential interference contrast imaging protocol 2007-10-09 2008-05-01 DIC Differential interference contrast imaging protocol Differential interference contrast microscopy Nomarski optical imaging protocol _7_7.4 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Phase contrast imaging protocol 2007-10-09 2008-05-01 Phase contrast imaging protocol Phase contrast microscopy _7_7.5 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Polarization contrast imaging protocol 2007-10-09 2008-05-01 Polarization contrast imaging protocol Polarization microscopy _7_7.6 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Total internal reflection imaging protocol 2007-10-09 2008-05-01 TIRM Total internal reflection imaging protocol Total internal reflection microscopy _7_7.7 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Intrinsic emission imaging protocol 2007-10-09 2007-10-09 Intrinsic emission imaging protocol Intrinsic emission microscopy _7_7.8 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Spectroscopic imaging protocol 2007-10-09 2007-10-09 Spectroscopic imaging protocol Spectroscopic microscopy _7_7.9 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Electron Energy Loss Spectroscopy imaging protocol 2007-10-09 2007-10-09 Electron Energy Loss Spectroscopy Electron Energy Loss Spectroscopy imaging protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Computer Axial Tomography imaging protocol 2007-10-09 2007-10-09 CAT CAT imaging protocol CT Imaging protocol Computer Axial Tomography imaging protocol _7_2.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Electrical recording protocol 2007-10-09 2007-10-09 Electrical recording protocol _7_3 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Micro-electrode recording protocol 2007-10-09 2007-10-09 Micro-electrode recording protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Macro-electrode recording protocol 2007-10-09 2007-10-09 Macro-electrode recording protocol _7_3.4 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Extracellular electrode recording protocol 2007-10-09 2007-10-09 Extracellular electrode recording protocol _7_3.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Intracellular electrode recording protocol 2007-10-09 2007-10-09 Intracellular electrode recording protocol _7_3.2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Ion channel recording protocol 2007-10-09 2007-10-09 Ion channel recording protocol _7_3.2.2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Amperometric electrode recording protocol 2007-10-09 2007-10-09 Amperometric electrode recording protocol _7_3.3 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Single electrode extracellular recording protocol 2007-10-09 2007-10-09 Single electrode extracellular recording protocol _7_3.1.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Grid electrode recording protocol 2007-10-09 2007-10-09 Grid electrode recording protocol _7_3.4 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Current clamp voltage recording protocol 2007-10-09 2007-10-09 Current clamp voltage recording protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Voltage clamp current recording protocol 2007-10-09 2007-10-09 Voltage clamp current recording protocol _7_3.2.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Single-electrode voltage clamp recording protocol 2007-10-09 2007-10-09 Single-electrode voltage clamp recording protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Whole-cell voltage clamp recording protocol 2007-10-09 2007-10-09 Whole-cell voltage clamp recording protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Multiple-electrode voltage clamp recording protocol 2007-10-09 2007-10-09 Multiple-electrode voltage clamp recording protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Cell-attached single-channel recording protocol 2007-10-09 2007-10-09 Cell-attached single-channel recording protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Cell-detached single-channel recording protocol 2007-10-09 2007-10-09 Cell-detached single-channel recording protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Cell-detached inside-out single-channel recording protocol 2007-10-09 2007-10-09 Cell-detached inside-out single-channel recording protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Cell-detached inside-out single-channel recording protocol 2007-10-09 2007-10-09 Cell-detached outside-out single-channel recording protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Reconstituted bilayer single-channel patch recording protocol 2007-10-09 2007-10-09 Reconstituted bilayer single-channel patch recording protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Reconstituted bilayer electrical recording protocol 2007-10-09 2007-10-09 Reconstituted bilayer electrical recording protocol http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Ion-sensitive electrode recording protocol 2007-10-09 2007-10-09 Ion-sensitive electrode recording protocol _7_3.3.2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated pH-sensitive electrode recording protocol 2007-10-09 2007-10-09 _7_3.3.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated pH-sensitive electrode recording protocol Cuff-electrode recording protocol 2007-10-09 2007-10-09 Cuff-electrode recording protocol Suction electrode recording protocol _7_3.4.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Field electrode recording protocol 2007-10-09 2007-10-09 Field electrode recording protocol Surface electrode recording protocol _7_3.4.2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Electroencephalography recording protocol 2007-10-09 2007-10-09 EEG Electroencephalography recording protocol _7_3.4.2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Electrocardiography recording protocol 2007-10-09 2007-10-09 ECG EKG Electrocardiography recording protocol _7_3.4.2_7_11.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated In-situ hybridization protocol 2007-10-09 2007-10-09 In-situ hybridization protocol _7_5.2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Indentifying value 2007-10-05 2007-10-05 Indentifying value http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary Accession number 2007-10-05 2007-10-05 Accession Accession number http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary Primary key 2007-10-05 2007-10-05 Primary key http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary Life Science Indenfier 2007-10-05 2007-10-05 LSID Life Science Indenfier http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary Computational model 2007-10-10 2007-10-10 A mathematical description of a inter-connected and/or dynamic biological system. Computational model _4_9 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Nerve cell model 2007-10-10 2007-10-10 A mathematical description of the structure or function of nerve cells and/or their cellular compartments. Computational neuronal model Nerve cell model http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2300 http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2302 http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2303 Nerve cell structural model 2007-10-10 2007-10-10 A mathematical description of the structure of nerve cells and/or their cellular compartments. Nerve cell structural model http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated neuronal structure model Nerve cell functional model 2007-10-10 2007-10-10 A mathematical description of the physiological funcion of nerve cells and/or their cellular compartments. Nerve cell functional model computational neuronal model http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated neuronal physiological model Ionic current model 2007-10-10 2007-10-10 A mathematical description of the temporal and voltage dependencies of particular, ion-selective membrane currents. Ionic current model Membrane current model http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Protein folding model 2007-10-10 2007-10-10 Protein folding model http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Network interaction model 2007-10-10 2007-10-10 Network interaction model http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Pathway model 2007-10-10 2007-10-10 Pathway model enzyme network model http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated regulatory network model signaling pathway model Gene regulatory network model 2007-10-10 2007-10-10 Gene network model Gene regulatory network model http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Physiological model 2007-10-10 2007-10-10 A mathematical description of the complex physical and temporal dependencies between a set of related biological entities and their immediated environment. Physiological model Physiological system model http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Structural model 2007-10-10 2007-10-10 A coordinate-based mathematical description of a collection of biological structures. Structural model http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Macroscopic anatomical structure model 2007-10-10 2007-10-10 A mathematical description of the structure of organs and organ regions. Finite element decomposition of anatomical structure Macroscopic anatomical structure model Mesh model of brain structure Wavelet-based multi-resolution decomposition of anatomical structure anatomical model http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Multi-cell model 2007-10-10 2007-10-10 A mathematical description of the temporal dependencies of a related set of biological cells Multi-cell model http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated tissue model Neural circuit model 2007-10-10 2007-10-10 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. Neural circuit model circuit model http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated nerve cell circuit model neural network model Body system model 2007-10-10 2007-10-10 A mathematical description of the temporal activity dependence of an extended set of tissues and cells across an entire organism. Body system model http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Sequence-based model 2007-10-10 2007-10-10 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. Sequence-based model http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Sequence homology model 2007-10-10 2007-10-10 A mathematical description of the phylogenetic relatedness of a set of nucleic acid sequences based on a correlative comparison of linear sequence. Sequence homology model homology model http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Hydrophobicity model 2007-10-10 2007-10-10 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. Hydrophobicity model http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated hydrophobicity analysis hydrophobicity plot Protein structure classification 2007-10-10 2007-10-10 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. Protein structure classification http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated protein classification Signal processing software 2007-10-09 2007-10-09 Signal processing software _7_17 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Signal processing algorithm 2007-10-10 2007-10-10 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. DSP algorithm Digital signal processing algorithm Signal processing algorithm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Pipeline processing software 2007-10-11 2007-10-11 Pipeline processing software http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated workflow processing software Graphical pipeline construction software 2007-10-11 2007-10-11 Graphical pipeline construction software http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Systems interoperability software 146952 2007-10-11 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". June 11, 2011 Systems interoperability software http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated GRID computing software 2007-10-11 2007-10-11 GRID computing software http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Portlet component 2007-10-11 2007-10-11 Portlet component http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Subject report 2007-10-11 2007-10-11 Subject report _7_12.2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary Human subject report 2007-10-11 2007-10-11 Human subject report http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary patient report Literature corpus 2007-10-09 A collection of unstructured, scientific literature. February 12, 2010 Literature corpus _1_4 _4_6.4 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated literature Lexical processing algorithm 2007-10-10 2007-10-10 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. Lexical processing algorithm Text-mining algorithm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Natural language processing algorithm 2007-10-11 2007-10-11 NLP 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. Natural language processing algorithm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#Wikipedia_defSource Part-of-speech tagging algorithm 2007-10-11 2007-10-11 Baum-Welch algorithm Brill Tagger POST 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. Part-of-speech tagging algorithm Viterbi algorithm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#Wikipedia_defSource Bibliographic database 2007-10-09 2007-10-09 A collection bibliographic records describing published works from the scientific literature which may or may not contain abstracts Bibliographic database _1_4 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Structured knowledge resource 2007-10-09 2007-10-09 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). Structured data resource Structured knowledge resource _1_4 _4_8 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Controlled vocabulary 2007-10-11 2007-10-11 Controlled vocabulary 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. Medical Subject Headings (MeSH) Systematized Nomenclature of Medicine (SNOMED) _2.4 _4_8.2 controllled terminology http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#Wikipedia_defSource terminology Classification scheme 2007-10-11 2007-10-11 Classification scheme PFAM Structural Classification of Proteins (SCOP) Structured grouping of entities based on a correspondence of derived physicochemical properties. http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Taxonomy 2007-10-11 2007-10-11 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. Taxonomy http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#Wikipedia_defSource Thesaurus 2007-10-11 2007-10-11 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 Frequency". Thesaurus Unified Medical Language System (UMLS) http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#Wikipedia_defSource Ontology 2007-10-11 2007-10-11 BIRNLex Basic Formal Ontology (BFO) Descriptive Ontology for Linguistic and Cognitive Engineering (DOLCE) Formal Model of Anatomy (FMA) Gene Ontology (GO) 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 OBO Ontology of Phenotypic Qualities (PATO) OBO Relations Ontology (OBO-RO) Ontology Subcellular Anatomy Ontology (SAO) _4_8.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#Wikipedia_defSource Research knowledgebase 2007-10-09 A collection research data arranged according to a structured semantic framework. Basic research knowledge base Basic research knowledge base Knowledge base Knowledgebase Research knowledge base Research knowledgebase September 10, 2009 _1_1.3 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Clinical knowledgebase 2007-10-09 2007-10-09 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. Clinical knowledge base Clinical knowledgebase Clinical research (translational) knowledge base Clinical research knowledge base Clinical research translational knowledge base _1_1.2.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BillBug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated License 2007-10-11 2007-10-11 License http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary Open-source license 2007-10-11 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). Open source license Open-source license September 10, 2009 _2.3_4 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary GNU General Public License 146107 2007-10-11 2007-10-11 GNU General Public License GPL June 14, 2011 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. _2.3_4.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary http://www.gnu.org/licenses/gpl-2.0.html GNU Lesser General Public License 2007-10-11 2007-10-11 GNU Lesser General Public License LGPL _2.3_4.2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary http://www.gnu.org/licenses/lgpl-2.1.html Simulation software 2007-10-11 2007-10-11 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. June 11, 2011 Simulation software _4_15 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Text-mining software 2007-10-11 2007-10-11 Text-mining software http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Mozilla Public License 2007-10-11 2007-10-11 MPL Mozilla Public License _2.3_4.2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary http://www.mozilla.org/MPL/MPL-1.1.html Apache License 2007-10-11 2007-10-11 Apache License _2.3_4.3 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary http://www.apache.org/licenses/LICENSE-2.0.html BSD License 2007-10-11 2007-10-11 BSD License Note as of 2006, the BSD License is equivalent to the MIT License _2.3_4.3 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary http://www.opensource.org/licenses/bsd-license.php MIT License 2007-10-11 2007-10-11 MIT License _2.3_4.3 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary http://www.opensource.org/licenses/mit-license.html Closed-source license 2007-10-11 2007-10-11 Any non open source license with restrictions on the source code. Closed source license Closed-source license Restricted license _2.3_5 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary Commercial license 2007-10-11 2007-10-11 Commercial license _2.3_5.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary Book 151334 2007-10-11 2007-10-11 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. Book June 14, 2011 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Book series volume 2007-10-11 2007-10-11 Book series volume http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Personal communication 2007-10-11 2007-10-11 Informal communication Personal communication http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM Conference proceeding 2007-10-11 2007-10-11 Conference proceeding http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM Discussion 2007-10-11 2007-10-11 Discussion 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). http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM Government publication 2007-10-11 2007-10-11 Government publication http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM Standard specification 2007-10-11 2007-10-11 Standard specification http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated standard spec standards document National standard specification 2007-10-11 2007-10-11 National standard specification government standard specification http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated International standard specification 2007-10-11 2007-10-11 International standard specification consortium standard specification http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated 2007-10-11 2007-10-11 Listserv or discussion group (as an entity, as opposed to a single discussion thread which uses the value "discussion") (NLM). http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM Patent 2007-10-11 2007-10-11 Patent http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM Thesis 2007-10-11 2007-10-11 Thesis http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM Website 2007-10-11 2007-10-11 Website http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM Portal 2007-10-11 2007-10-11 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. Portal _1_5 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#Wikipedia_defSource Organization portal 2007-10-11 2007-10-11 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. Institution portal Organization portal _1_5.4 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Department portal 2007-10-11 2007-10-11 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. Department portal _1_5.3 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Laboratory portal 2007-10-11 2007-10-11 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. Laboratory portal _1_5.3 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Topical portal 2007-10-11 A portal where the aggregated resources are restricted to those describing or related to a particular topic. Information portal September 10, 2009 Topical portal _1_5.5 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Disease-related portal 2007-10-11 2007-10-11 A portal where the aggregated resources are restricted to those describing or related to a particular disease. Disease-related portal http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Patient-support portal 2007-10-11 2007-10-11 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. Patient-advocate portal Patient-support portal http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Research forum portal 2007-10-11 2007-10-11 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. AlzForum Research forum portal Schizophrenia Research Forum http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Link aggregation site 2007-10-11 2007-10-11 A web site containing a curated set of links typically focussed on a particular topic or set of related topics. Link aggregation site Link classification site Link clustering site http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated Citation record element 2007-10-11 2007-10-11 Citation record element Those elements defined as a part of the PubMed DTD and used by many literature citation databases _4_6.2 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM Title set 2007-10-11 2007-10-11 Title set http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM Abstract 2007-10-11 2007-10-11 Abstract _4_6.1 http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM Author set 2007-10-11 2007-10-11 Author set http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM Title 2007-10-11 2007-10-11 Title http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM primary title Alternative title 2007-10-11 2007-10-11 Alternative title alt title http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM secondary title Author 2007-10-11 2007-10-11 Author http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM Author affiliation 2007-10-11 2007-10-11 Author affiliation author adress http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM Group author 2007-10-11 2007-10-11 Group author collaborative author http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM Grant number 2007-10-11 2007-10-11 Grant number http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM Grant sponsor 2007-10-11 2007-10-11 Grant sponsor http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#NLM