Bill Bug The BIRN project lexicon Duplicated all SKOS core:prefLabel Annotations as rdfs:label Annotations using a parsing script supplied by Trish Whetzel (UPenn/OBI community). This makes it possible to use rdfs:label as the DISPLAY_SLOT in Protege to match OBI and to use it to generate OWLDocs where both BIRNLex and OBI classes will use the same AnnotationProperty for their preferred display name (BB: 2007-02-27). Maryann Martone 1.2 The BIRN Ontology Task Force Jessica Turner David Kennedy Jeff Grethe en The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. It is built using the organizational framework provided by the foundational Basic Formal Ontology (BFO). It uses an abstract biomedical layer on top of that - OBO-UBO which has been constructed as a proposal to the OBO Foundry. This is meant to support creating a sharable view of core biomedical objects such as biomaterial_entity, and organismal_entity that all biomedical ontologies are likely to need and want to use with the same intended meaning. The BIRNLex biomaterial entities have already been factored to separately maintained ontology - BIRNLexBiomaterialEntity.owl which this BIRNLex-Main.owl file imports. The Ontology of Biomedical Investigation (OBI) is also imported and forms the foundation for the formal description of all experiment-related artifacts. The BIRNLex will serve as the basis for construction of a formal ontology for the multiscale investigation of neurological disease. 2006-07-28 Christine Fennema-Notestine 2007-03-07 Carol Bean Amarnath Gupta BIRNLex-Main The current (2006-10-10) members of the BIRN Ontology Task Force are listed here as the primary curators of the main BIRNLex ontology. Others from within BIRN labs and directly collaborating with BIRN labs have also contributed to specific classes and class properties. Effort is made to provide attribution for each class, where appropriate. Assessment Jessica Turner BF_T0000276 Assessment curation complete 2006-06-01 2006-10-11 OBI_69 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. C0036341 uncurated 2006-06-01 OBI_155 2006-10-11 Schizophrenia UMLS Schizophrenia A severe emotional disorder of psychotic depth characteristically marked by a retreat from reality with delusion formation, hallucinations, emotional disharmony, and regressive behavior. (MeSH) Jessica Turner Handedness BF_T0000316 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) 2006-10-11 UMLS pending final vetting 2006-04-04 Handedness Maryann Martone BIRN OTF This list contains precoordinated terms that will be addressed at a future date. 2006-10-11 Behavioral paradigm in which the subject ingests food. Eating_paradigm uncurated BF_T0000265 2006-06-01 Jessica Turner Acupuncture_paradigm 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 Angie Laird BrainMap.org 2006-06-01 graph position temporary BF_T0000339 2006-10-11 BF_T0000338 BrainMap.org 2006-06-01 Action_observation_paradigm 2006-10-11 Action Observation Jessica Turner A behavioral paradigm in which subjects view images of moving body parts (Brain Map). pending final vetting Clarify the exact nature of this task Action_observation_paradigm Mismatch_negativitiy_paradigm Mismatch_negativitiy_paradigm behavioral paradigm that assesses a response to non-attended stimuli which are dissimilar to the majority of stimuli presented. 2006-10-11 Jessica Turner BF_T0000357 Jessica Turner 2006-06-01 2006-10-11 Eating_paradigm Angie Laird uncurated BrainMap.org curation complete BrainMap.org BF_T0000271 2006-06-01 Jessica Turner Breathhold_paradigm 2006-10-11 A behavioral paradigm that requires subjects to hold their breath one or more times. Breathhold_paradigm Angie Laird This term does not differentiate between lexical and semantic parsing by the subject Reading_paradigm 2006-06-01 pending final vetting BF_T0000361 Reading_paradigm A behavioral paradigm in which a subject is asked to read either silently (covert) or aloud (overt) BrainMap.org A behavioral paradigm in which a subject makes a rapid eye movement relative to an initial target (JB). 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. Jyl Boline Eye_Saccade_paradigm 2006-10-11 BF_T0000360 Eye_Saccade_paradigm pending final vetting 2006-06-01 Maryann Martone 2006-05-15 Electron_microscopic_imaging_assay 2006-10-11 Electron_microscopic_imaging_assay BIRN OTF uncurated Microscopic_imaging_assay uncurated 2006-05-15 BIRN OTF Microscopic_imaging_assay OBI_185 2006-10-11 BIRN OTF Changed name from the ambiguous Biochemical_protocol to Biochemical_specimen_preparation_protocol (BB). Biochemical_speciment_preparation_protocol Biochemical_speciment_preparation_protocol 2006-10-11 Bill Bug 2006-06-01 C0023114 Behavioral_laterality Behavioral_laterality 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. Behavioral_phenotype 2006-10-11 Behavioral_phenotype uncurated 2006-06-01 BIRN OTF 2006-04-04 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) 2006-10-11 pending final vetting Jeff Grethe UMLS Maryann Martone 2006-05-15 Microdissection 2006-10-11 C0598304 Microdissection uncurated 2006-05-15 Laser_capture Maryann Martone 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) C1113652 uncurated 2006-10-11 Laser_capture 2006-10-11 BIRN OTF Imaging_platform Imaging_platform OBI_50 2006-06-01 2006-06-01 2006-10-11 BIRN OTF Magnetic_resonance_imaging_platform Magnetic_resonance_imaging_platform uncurated 2006-06-01 2006-10-11 Functional_MRI_platform BIRN OTF Functional_MRI_platform uncurated Structural_MRI_platform BIRN OTF 2006-06-01 2006-10-11 uncurated Structural_MRI_platform uncurated 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) C0009932 2006-10-11 OBI_176 Control_group UMLS Control_group Maryann Martone uncurated 2006-06-01 2006-10-11 Episodic_recall_paradigm Angie Laird uncurated BrainMap.org Episodic_recall_paradigm A behavioral paradigm in which subjects recall items from episodic memory (autobiographical history, long-term event memories). Jessica Turner 2006-06-01 OBI_29 2006-10-11 2006-05-15 BIRN OTF Specimen_preparation_protocol Specimen_preparation_protocol Bill Bug C0200363 uncurated C0200363 uncurated Maryann Martone UMLS A behavioral phenotype where the subject preferentially uses the left hand for tasks requiring the use of a single hand or a dominant hand. 2006-10-11 Left_handedness Left_handedness 2006-04-04 C0234418 nnnnnn 2006-10-11 uncurated Molecular_phenotype 2006-06-01 BIRN OTF Molecular_phenotype 2006-06-01 Gene_expression_phenotype uncurated Gene_expression_phenotype 2006-10-11 BIRN OTF 2006-10-11 Item_recognition_paradigm Jessica Turner 2006-10-11 pending final vetting Item_recognition_paradigm 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. Bill Bug uncurated bfo:process BIRN OTF Behavioral_process 2006-10-11 Behavioral_process 2006-05-15 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 Reagent BIRN OTF 2006-05-15 OBI_258 2006-10-11 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) uncurated C0034760 Fixative uncurated 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) C0016184 2006-05-15 BIRN OTF 2006-10-11 Maryann Martone 2006-10-11 i.p. Intraperotineal_injection Maryann Martone Intracellular_injection BF_T0000117 2006-06-01 Subthelial_injection uncurated Maryann Martone Subthelial_injection 2006-10-11 2006-06-01 Maryann Martone 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 2006-10-11 uncurated Intraperotineal_injection 2006-10-11 2006-06-01 uncurated Bill Bug administration of a drug via injection into a muscle. (CSP) 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 Maryann Martone i.m. C0021492 Intramuscular_injection 2006-10-11 2006-06-01 C0021492 uncurated Intrathecal_injection uncurated C0021896 2006-06-01 C0021896 Intrathecal_injection BF_T0000184 uncurated Maryann Martone Collaborator 2006-07-15 2006-10-11 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. 2006-10-11 uncurated Role played by individual investigators during the course of an investigation Maryann Martone Investigator_role 2006-07-15 Investigator_role Jessica Turner BrainMap.org Angie Laird 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. 2006-10-11 Delayed_matching_to_sample_paradigm BF_T0000346 Delayed_matching_to_sample_paradigm uncurated 2006-06-01 In what way is this related to Happiness? Is there in fact a single underlying Cognitive_entity for which Happiness and Sadness are just either end of the quality gamut describing that entity as experienced by an individual (BB)? Can you experience both Happiness and Sadness simultaneously (BB)? Bill Bug uncurated BIRN OTF 2006-06-01 C0233486 Sadness Sadness 2006-10-11 C0232478 2006-10-11 Ingestion Ingestion Bill Bug uncurated 2006-06-01 C0232478 Maryann Martone BF_T0000150 2006-06-01 Sham_operated_control_group 2006-10-11 A subject group that has received an identical surgical procedure to the experimental group but without the treatment under study. Sham_operated_control_group Maryann Martone uncurated 2006-05-15 2006-10-11 Transmission_electron_microscope definition incomplete 2006-10-11 2006-05-15 uncurated Electron_microscope BIRN OTF C0262879 Electron_microscope C0262880 Maryann Martone Transmission_electron_microscope 2006-05-15 uncurated pentanedial Maryann Martone 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) Bill Bug 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) Glutaraldehyde 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) 2006-10-11 A crosslinking fixative. Glutaraldehdye is a pentanedial; 5-carbon saturated chain with a highly reactive aldehyde group on each end (MM). C0017814 glutaral glutardialdehyde Glutaraldehyde C0017814 uncurated Memory 2006-05-15 uncurated MeSH-UMLS 2006-10-11 Cognitive_process uncurated 2006-05-15 Cognitive_process BIRN OTF Attention Jessica Turner 2006-10-11 C0004268 The process of focusing on certain aspects of current experience to the exclusion of others. It is the act of heeding or taking notice or concentrating. (MeSH) Attention BF_T0000216 2006-10-11 Memory The cognitive process of encoding, storing and retrieving past experience Jessica Turner 2006-05-15 2006-06-01 2006-10-11 BIRN OTF Covert_braille_reading_paradigm BrainMap.org 2006-10-11 Covert_braille_reading_paradigm pending final vetting Jessica Turner A behavioral paradigm in which a subject reads aloud with fingers. Angie Laird 2006-06-01 BF_T0000341 Brain Map lists only a Braille reading paradigm but BIRNLex is dividing this into overt and covert Braille reading paradigms Covert_visual_reading_paradigm uncurated Covert_visual_reading_paradigm BIRN OTF 2006-06-01 California_Verbal_Learning_Test California_Verbal_Learning_Test definition incomplete BF_T0000220 2006-10-11 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 Angie Laird DMTS 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). 2006-10-11 pending final vetting 2006-06-01 BrainMap.org BF_T0000359 moved under the new Item_recognition_paradigm class (BB). Sternberg_paradigm Sternberg_paradigm Jessica Turner Need to clarify what a Sternberg paradigm involves delayed match-to-sample paradigm Bill Bug 2006-06-01 curation complete 2006-10-11 Brett Peterson C0002045 A well defined set of rules that can be expressed using formal mathematical expression and thereby implemented in a computing environment. Algorithm UMLS Algorithm Sensorimotor_paradigm A behavioral paradigm that requires the subject respond to stimuli that are dissimilar to the majority of stimuli presented 2006-06-01 BF_T0000266 Sensorimotor_paradigm curation complete Jessica Turner 2006-10-11 Multiphoton_microscope Optical microscope 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. 2006-10-11 2006-05-15 Multiphoton_microscope uncurated Maryann Martone BF_T0000028 Jessica Turner Autobiographical_memory 2006-10-11 Memory that involves the conscious recall or recognition of one’s own life. Autobiographical_memory C0561843 2006-05-15 uncurated 2006-05-15 Ultrahigh_voltage_electron_microscope Transmission electron microscope capable of operating at an accelerating voltage of > 1 MeV 2006-10-11 BIRN OTF BF_T0000031 Ultrahigh_voltage_electron_microscope uncurated Tissue_section 2006-05-15 Maryann Martone 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. uncurated OBI_261 BF_T0000134 Tissue_section 2006-10-11 OBI_94 Specimen_fixation 2006-07-15 BF_T0000236 2006-07-15 MeSH Specimen_fixation pending final vetting 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) Maryann Martone 2006-06-01 Trail_making_test Christine Fennema-Notestine Trail_making_test 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 ...). 2006-10-11 curation complete uncurated Microscope C0181839 BIRN OTF Microscope An instrument used to obtain a magnified image of small objects and reveal details of structure not otherwise distinguishable. 2006-10-11 Imaging_instrument BIRN OTF uncurated 2006-05-15 Imaging_instrument OBI_47 2006-10-11 UMLS 2006-05-15 BF_T0000034 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) uncurated 2006-05-15 Maryann Martone 2006-10-11 Monoclonal_antibody Monoclonal_antibody Immunoglobulin that is used as a reagent to localize a signal through an immunological reaction. Antibody BF_T0000132 Antibody antibody used for immunocytochemical protocol uncurated Maryann Martone 2006-10-11 2006-05-15 2006-10-11 pending final vetting BF_T0000231 The cognitive process of remembering/recollecting previously learned material without aid of any external cues. 2006-05-15 Christine Fennema-Notestine Free_recall Free_recall 2006-10-11 2006-07-15 uncurated 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 BF_T0000183 Project_leader Maryann Martone 2006-05-15 2006-10-11 Intracellular_injection_protocol Intracellular_injection_protocol BIRN OTF uncurated Jessica Turner Simple_saccade_paradigm 2006-06-01 Angie Laird 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) This term is equivalent to "saccade paradigm" in Brain Map BIRN OTF 2006-10-11 uncurated BrainMap.org 2006-10-11 Anti_saccade_paradigm Anti_saccade_paradigm Anti-saccades paradigm Jessica Turner 2006-06-01 BIRN OTF Angie Laird 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) BF_T0000341 pending final vetting Simple_saccade_paradigm BrainMap.org Auditory_oddball_paradigm 2006-10-11 2006-06-01 Auditory_oddball_paradigm An oddball discrimination paradigm that involves responding to auditory stimuli that are dissimilar to the majority of auditory stimuli presented. Jessica Turner curation complete uncurated UMLS