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 Neuropsychological_assessment Christine Fennema-Notestine Neuropsychological_assessment 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) 2006-10-11 C0027902 2006-06-01 2006-10-11 BIRN OTF Memory_phenotype uncurated 2006-06-01 Memory_phenotype 2006-06-01 2006-10-11 uncurated Working_memory_phenotype BIRN OTF Working_memory_phenotype Substances used in radiography that allow visualization of certain tissues. (CSP) Bill Bug uncurated Contrast_agent Contrast_agent 2006-05-15 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) 2006-10-11 C0009924 BIRN OTF C0009924 Substances used in radiography that allow visualization of certain tissues. (MeSH) Normal_control_group uncurated Normal_control_group 2006-10-11 2006-06-01 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 Maryann Martone uncurated BF_T0000148 Sham_control_group 2006-06-01 Sham_control_group 2006-10-11 a placebo-treated control group A subject group that has received an identical treatment to the experimental group but without the active agent under study. Maryann Martone 2006-10-11 2006-05-15 Agent_delivery_process curation complete Agent_delivery_process Maryann Martone injection of drug The process by which an experimental agent is delivered to an organism or part of organism. ingestion of toxin bfo:process BF_T0000274 Divided_auditory_attention_paradigm Divided_auditory_attention_paradigm 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. Angie Laird uncurated BrainMap.org BF_T0000347 Jessica Turner 2006-06-01 2006-10-11 Maryann Martone C0039294 C0039294 2006-10-11 Tannic_acid 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). Tannic_acid 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) 2006-05-15 uncurated UMLS Right_handedness 2006-10-11 2006-04-04 C0234417 uncurated UMLS A behavioral phenotype where the subject preferentially uses the right hand for tasks requiring the use of a single hand or a dominant hand. Maryann Martone Right_handedness Nicotine_use_assessment BIRN OTF uncurated 2006-10-11 2006-06-01 Nicotine_use_assessment BIRN OTF Optical_microscope 2006-10-11 2006-05-15 ssss uncurated Optical_microscope Organism_attribute Bill Bug BIRN OTF 2006-10-11 Organism_attribute uncurated 2006-06-01 2006-10-11 BIRN OTF Organism_characteristic OBI_3 This class and it's children are essentially replaced via the use of PATO. Many of the 'Phenotype' classes are given as 'Behavioral_activity' and 'Behavioral_function' classes in BIRNLex-CogBehavior.owl (BB:2007-03-07). 2006-07-15 Organism_characteristic What is this and how would it differ from Phenotype_attribute (BB)? 2006-05-15 BIRN OTF Gene_specific_probe uncurated BIRN OTF Gene_specific_probe 2006-05-15 2006-10-11 2006-10-11 uncurated RNA_specific_probe 2006-05-15 RNA_specific_probe BIRN OTF 2006-10-11 DNA_specific_probe DNA_specific_probe uncurated 2006-10-11 transmission electron microscope cabable of operating an accelerating voltage in the range of 500- 1000 KeV uncurated BF_T0000029 2006-05-15 BIRN OTF High_voltage_electron_microscope High_voltage_electron_microscope 2006-10-11 Serial_item_recognition_paradigm BF_T0000219 Serial_item_recognition_paradigm 2006-06-01 uncurated SIRP moved under the new Item_recognition_paradigm class (BB). Bill Bug 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). Jessica Turner BIRN OTF Behavioral_assessment 2006-10-11 Behavioral_assessment 2006-06-01 uncurated Immunolabeling_protocol uncurated 2006-10-11 2006-05-15 Immunolabeling_protocol BIRN OTF uncurated 2006-06-01 Smoking_behavior Smoking_behavior BIRN OTF 2006-10-11 2006-10-11 uncurated Past_smoking_behavior pending final vetting Past_smoking_behavior C0337664 2006-10-11 pending final vetting 2006-06-01 Jessica Turner Smoking Behavioral phenotype used to describe an individual who currently smokes tobacco products. Smoking 2006-06-01 former smoking behavior ex smoking behavior A behavioral phenotype used to describe an individual who is currently not smoking tobacco products but has at some time in the past. C0337671 2006-10-11 BIRN OTF BIRN OTF Never_has_smoked Never_has_smoked 2006-06-01 Behavioral phenotype used to describe an individual who has never smoked tobacco products. Christine Fennema-Notestine The memory that someone or something present has been previously encountered. (MeSH) uncurated 2006-05-15 C0524637 Recognition_memory Recognition_memory MeSH-UMLS 2006-10-11 uncurated 2006-06-01 Phenotype Phenotype 2006-10-11 BIRN OTF How does this related to Phenotype_attribute and to PaTO expressions (BB)? Bill Bug 2006-10-11 UMLS The affective response to an actual current external danger which subsides with the elimination of the threatening condition. (MeSH) Fear C0015726 uncurated Jessica Turner 2006-06-01 Unpleasant but normal emotional response to genuine external danger or threats; compare with ANXIETY and CLINICAL ANXIETY. (CSP) Fear C0015726 Bill Bug 2006-10-11 Collaborating_institution 2006-04-04 bfo:object_aggregate Institution Maryann Martone 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). 2006-04-04 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. graph position temporary 2006-10-11 Institution Bill Bug 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. Maryann Martone Collaborating_institution graph position temporary Jessica Turner 2006-06-01 Angie Laird 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 Deductive_reasoning_paradigm 2006-10-11 BrainMap.org uncurated Tissue_dissection Tissue_dissection uncurated OBI_94 2006-10-11 BIRN OTF 2006-05-15 Injection 2006-10-11 uncurated C0021485 C0021485 Injection Maryann Martone 2006-06-01 _birnlexMain_retired_class Bill Bug These are classes for which the represented entities are now described using a different class. A class is deprecated if it's semantic meaning required alteration or its entity is now represented directly in an imported foundational ontology. Such obseleted classes are removed from the core subsumptive hierarchy and retired to this root branch of the tree for this ontology. Deprecated classes maintain their original identifiers, so as to provide support for previous applications making use of the class prior to its being deprecated. 2007-03-07 2007-03-07 _birnlexMain_retired_class uncurated 2006-05-15 Maryann Martone Polyclonal_antibody 2006-10-11 Polyclonal_antibody 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) BF_T0000035 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). Changed preferred Label from Contrast_enhancement_protocol to Microscopy_contrast_enhancement_protocol. 2006-05-15 uncurated Microscopy_contrast_enhancement_protocol Bill Bug BIRN OTF Microscopy_contrast_enhancement_protocol 2006-10-11 BF_T0000261 2006-10-11 Experimental_paradigm 2006-06-01 Jessica Turner Experimental_paradigm uncurated Genotype BIRN OTF 2006-10-11 Bill Bug Genotype definition incomplete 2006-06-01 Maryann Martone Lead_institution graph position temporary 2006-10-11 Lead_institution 2006-04-04 Bill Bug Christine Fennema-Notestine Mild_cognitive_impairment 2006-06-01 2006-10-11 BF_T0000227 uncurated Mild_cognitive_impairment 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_T0000225 Christine Fennema-Notestine curation complete A cognitive phenotype measuring an individual's facility with producing spoken language. 2006-06-01 Verbal_fluency Verbal_fluency Cognitive_phenotype Cognitive_phenotype 2006-10-11 BIRN OTF uncurated 2006-06-01 2006-10-11 Anxiety Persistent feeling of dread, apprehension, and impending disaster (MeSH). 2006-06-01 2006-10-11 MeSH Jessica Turner C0003467 C0003467 Anxiety UMLS uncurated 2006-10-11 Working_memory Memory that involves the conscious encoding, storing and retrieving information encountered recently uncurated BF_T0000218 Working_memory 2006-05-15 Jessica Turner Oddball_discrimination_paradigm Jessica Turner 2006-06-01 2006-10-11 Oddball_discrimination_paradigm A behavioral paradigm that assesses a response to non-attended stimuli which are dissimilar to the majority of stimuli presented curation complete BF_T0000267 An oddball discrimination paradigm where subjects view letters or objects and indicate when they see a target stimulus. uncurated Angie Laird Visual_oddball_paradigm BF_T0000340 BrainMap.org Visual_oddball_paradigm Jessica Turner Ambidextrous Maryann Martone C0023114 Ambidextrous 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. 2006-04-04 UMLS pending final vetting Jessica Turner A mental state that arises spontaneously rather than through conscious effort and is often accompanied by physiological changes; a feeling. uncurated UMLS Bill Bug Cognitive_entity Describes entities related to cognitive processes. At some point, this will have to be merged with the OBR but for now I think it's best kept separate (MM). Maryann Martone Moved from base of hiearchy to a subclass of bfo:realizable_entity (BB). 2006-10-11 Cognitive_entity 2006-06-01 bfo:realizable_entity uncurated C0013987 Emotion 2006-10-11 2006-06-01 C0013987 Emotion 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. Drawing_paradigm uncurated BF_T0000356 BrainMap.org 2006-06-01 Jessica Turner Drawing_paradigm Angie Laird Vascular_perfusion BF_T0000032 2006-06-01 2006-10-11 uncurated Vascular_perfusion 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). Method of agent delivery where the agent is pumped through the vasculature of the animal. Maryann Martone BIRN OTF Protein_specific_probe 2006-05-15 Protein_specific_probe 2006-10-11 uncurated Angie Laird 2006-06-01 2006-10-11 Encoding_paradigm BF_T0000358 BrainMap.org Encoding_paradigm Jessica Turner A behavioral paradigm in which a subject views stimuli (words, pictures, letters) and are instructed to memorize them. uncurated Classical_conditioning_paradigm Classical_conditioning_paradigm 2006-10-11 BrainMap.org BF_T0000343 Angie Laird uncurated 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. Jessica Turner 2006-06-01 Principal_investigator Maryann Martone 2006-10-11 Principal_investigator BF_T0000157 2006-07-15 uncurated 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 A process for delivering an agent to an object of study in which the object is physically submersed in the agent. 2006-06-02 C0020940 UMLS Maryann Martone Immersion uncurated Immersion immersion of a tissue sample into fixative 2006-10-11 C0020940 Non_smoking C0337672 2006-10-11 UMLS BIRN OTF 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. Non_smoking 2006-06-01 pending final vetting Changed name to singular from plural to comply with univocity constraint (BB). definition incomplete 2006-06-01 Quantitative_organism_attribute Quantitative_organism_attribute Bill Bug 2006-10-11 BIRN OTF 2006-06-01 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. BrainMap.org definition incomplete BF_T0000262 Behavioral_paradigm graph position temporary Behavioral_paradigm Jessica Turner Angie Laird 2006-10-11 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). Maryann Martone 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. 2006-10-11 C0040549 2006-05-15 Toxin uncurated Toxin C0002957 Jessica Turner 2006-06-01 uncurated A strong emotional feeling of displeasure aroused by being interfered with, injured or threatened (MeSH). MeSH C0002957 2006-10-11 Anger Anger UMLS BF_T0000272 Age curation complete 2006-10-11 The measurable time of existence of an organism. C0001779 2006-10-11 BIRN OTF C0001779 Age Postnatal_age 2006-10-11 2006-10-11 curation complete Postnatal_age BIRN OTF Embryonic_age curation complete Embryonic_age BF_T0000273 2006-10-11 The measureable time of existence since conception and before birth 2006-10-11 BIRN OTF The measurable time of existence of an organism from the point of birth Fagerstrom_test_for_nicotine_dependence 2006-06-01 uncurated is an assessment which consists of a questionnaire that measures nicotine use (Fagerstrom citation) 2006-10-11 Fagerstrom_test_for_nicotine_dependence C0451156 Jessica Turner BIRN OTF uncurated C0005910 Body_weight 2006-10-11 C0005910 Body_weight A measure of the mass of the entire body of the organism. 2006-06-01 2006-10-11 BIRN OTF uncurated Transmission_electron_microscopic_imaging_assay Transmission_electron_microscopic_imaging_assay Maryann Martone 2006-05-15 C0024554 C0024554 Female C0015780 Maryann Martone Female 2006-10-11 2006-06-01 A member of the sex which conceives and gives birth to young, or (in a wider sense) which produces ova (fro m Online Medical Dictionary) Maryann Martone The sex of an organism. Conceptually broad term; should probably break this down at least to phenotypic gender and genotypic gender 2006-06-01 2006-10-11 C0079399 Gender uncurated C0079399 Gender C0015780 Male Maryann Martone 2006-10-11 A member of the sex which produces sperm. The "sperm" is defined as the smaller gamete in a heterogamous reproduction system, while the larger gamete is produced by the female. (wikipedia) 2006-06-01 Male Bill Bug BIRN OTF Phenotype_attribute 2006-06-01 Phenotype_attribute 2006-10-11 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). definition incomplete In_column_energy_filter 2006-06-01 2006-10-11 In_column_energy_filter BIRN OTF Energy_filter Energy_filter BIRN OTF 2006-10-11 uncurated 2006-06-01 Cardinal_part_of_microscope uncurated Cardinal_part_of_microscope 2006-10-11 BIRN OTF OBI_36 2006-10-11 uncurated Cardinal_part_of_imaging_instrument Cardinal_part_of_imaging_instrument BIRN OTF 2006-06-01 2006-06-01 uncurated 2006-06-01 2006-10-11 2006-10-11 BIRN OTF uncurated Specimen_preparation Specimen_preparation OBI_69 2006-06-01 Sample_dissection Sample_dissection BIRN OTF uncurated uncurated Laser_scanning_confocal_microscope Maryann Martone 2006-05-15 Laser_scanning_confocal_microscope 2006-10-11 BF_T0000022 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) 2006-05-15 2006-10-11 Confocal_microscope Confocal_microscope uncurated BIRN OTF UMLS BIRN OTF OBI_155 uncurated Neurodegenerative_disease 2006-07-15 2006-10-11 Neurodegenerative_disease BIRN OTF uncurated 2006-06-01 Image_analysis_software Image_analysis_software 2006-10-11 2006-10-11 Electron_tomography_software Maryann Martone Electron_tomography_software 2006-06-01 Image_reconstruction_software BIRN OTF uncurated 2006-10-11 Image_reconstruction_software uncurated 2006-05-15 2006-10-11 A transformation that applies an algorithm with specified parameters on a data set on a specific computing platform. OBI_95 Algorithm_execution Algorithm_execution 2006-06-01 Jeff Grethe curation complete uncurated Experimenter 2006-10-11 Experimenter Maryann Martone 2006-07-15 BIRN OTF Staining_protocol Staining_protocol uncurated 2006-10-11 2006-05-15 uncurated BF_T0000131 2006-10-11 curation complete 2006-06-01 Image_reconstruction_algorithm Image_reconstruction_algorithm Maryann Martone Algorithm used to compute a reconstruction from a set of images, e.g., R-weighted back projection. BF_T0000139 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. 2006-06-01 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. R-weighted_back_projection R-weighted_back_projection Maryann Martone 2006-10-11 2006-10-11 BIRN OTF Physical_phenotype Physical_phenotype uncurated 2006-06-01 Scanning_electron_microscope 2006-05-15 2006-10-11 uncurated Scanning_electron_microscope C0262878 BIRN OTF Alzheimers_disease BIRN OTF Alzheimers_disease 2006-04-04 A neurodegenerative disease resulting in the insidious onset of dementia. Impairment of memory, judgement, attention span, and problem solving skills are followed by severe APRAXIAS and a global loss of cognitive abilities. The condition primarily occurs after age 60, and is marked pathologically by severe cortical atrophy and the triad of SENILE PLAQUES; NEUROFIBRILLARY TANGLES; and NEUROPIL THREADS. (From Adams et al., Principles of Neurology, 6th ed, pp1049-57) (adapted from MSH) 2006-10-11 MeSH C0002395 curation complete BIRN OTF Staining uncurated 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. 2006-06-01 Bill Bug 2006-10-11 Staining Gross_dissection uncurated 2006-05-15 Gross_dissection 2006-10-11 Maryann Martone 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) Phalloidin UMLS C0031312 uncurated Maryann Martone Phalloidin 2006-10-11 2006-05-15 uncurated Sample_sectioning 2006-06-01 2006-10-11 Sample_sectioning BIRN OTF 2006-06-01 uncurated Cognitive_assessment 2006-10-11 Jessica Turner C0870300 C0870300 UMLS Cognitive_assessment Christine Fennema-Notestine 2006-10-11 Verbal_fluency_assessment 2006-06-01 pending final vetting BF_T0000225 Verbal_fluency_assessment 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. uncurated 2006-10-11 Data_analyzer 2006-07-15 Maryann Martone Data_analyzer uncurated Maryann Martone 2006-06-01 2006-10-11 Gender_phenotype The observable physical characteristics typical of the male or female of the species. Gender_phenotype Light_microscopic_imaging_assay BIRN OTF Light_microscopic_imaging_assay 2006-10-11 uncurated 2006-05-15 BF_T0000030 2006-10-11 Intermediate_voltage_electron_microscope uncurated 2006-05-15 Intermediate_voltage_electron_microscope Maryann Martone Transmission electron microscope cabable of operating at an accelerating voltage in the range of 300-400 KeV 2006-10-11 2006-07-15 uncurated Instrument_operator Maryann Martone Instrument_operator BIRN OTF Protein_expression_phenotype 2006-10-11 2006-06-01 Protein_expression_phenotype uncurated Paraformaldehyde UMLS Paraformaldehyde 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). C0070066 Maryann Martone uncurated Bill Bug 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) uncurated Free_recall_ability Free_recall_ability 2006-10-11 2006-06-01 BIRN OTF definition incomplete 2006-10-11 Mini_mental_state_examination 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) Christine Fennema-Notestine BF_T0000222 Mini_mental_state_examination MMSE 2006-06-01 bfo:process 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. BF_T0000189 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) 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). 2006-04-04 Not sure whether this is the same as study; needs clarification (MM). Bill Bug BIRN OTF pending final vetting Experiment Maryann Martone 2006-10-11 Magnetic_resonance_imaging_scanner Magnetic_resonance_imaging_scanner BIRN OTF uncurated 2006-10-11 2006-05-15 Should look to FBbi for content here, hopefully brought into BIRNLex-Main via import. Fixation_protocol Fixation_protocol 2006-05-15 BIRN OTF uncurated 2006-10-11 2006-07-15 Co-investigator uncurated Co-investigator 2006-10-11 Maryann Martone uncurated C0018592 Jessica Turner 2006-06-01 2006-10-11 Happiness C0018592 UMLS Happiness Highly pleasant emotion characterized by outward manifestations of gratification; joy 2006-05-15 Maryann Martone Tissue_sectioning 2006-10-11 uncurated Tissue_sectioning 2006-06-01 2006-10-11 Image_processing_software uncurated BIRN OTF Image_processing_software