Model	Protocols
Submitter	LNI Account
Version	Version 5 (2007/05/31)
Namespace	urn:bml/brainml.org:internal/Protocols/5
Comments	Modified catalog_interaction schema and controlled vocabulary terms.
View	Structure   Vocabulary   (with IDs)

This is a tabular description of the controlled vocabulary values allowed for entries to fields in the data model. Also available in XML format.

Domains of Applicability

coverage data type functional context disease neurobiological_focus stage neural structure level_or_component structure / location organism resource availability access license method terminology resource type technique

Vocabulary Terms

resource type     data resource (neuroscience data or findings)          database (data sets)            Indexed research data, focusing on individual characteristics of particular instances.          atlas (spatially-organized data)            A spatially-indexed collection of images and possibly related metadata.          knowledge base (findings/knowledge derived from data)            Searchable reference focusing on findings / knowledge derived from data (scientific sense) -or- focusing on properties of standard types and categories rather than particular instances (computer science sense).              clinical knowledge base (diagnosis/treatment)                Knowledge base of clinical data.     bibliographic resource (library/publisher or literature access)       Library, collection, or access point for scientific literature.     software resource (software for acquisition, analysis, display or modeling)       A piece of software for handling neuroscience research data. May be an application, tool, plug-in, or other type of package.          data acquisition software            Software related to acquisition.          data processing/analysis/archiving software            Software for analyzing or otherwise processing data, or storing or archiving it, including format conversion.              software for time-series analysis (nonimage)                Software for time series data processing.              software for spatial/image analysis                Software for image data processing.              software for sequence analysis                Software for sequence analysis.              software for pathway analysis                Software for pathway analysis.          visualization software            Software for visualizing data.              3D/4D visualization                Software for 3D/4D visualization.          modeling/simulation software            Software for modeling or simulating a system's functioning.     research supplies (access to materials)       Materials or equipment for carrying out neuroscience research, or vendor of.          instrumentation            Instruments or devices.          organism            Organisms for use in research.          cell line/tissue            Cell line or tissue products.          reagent/chemical            Chemical or biological substances.     portal (access to people, places, or sites)       A resource pointing to or characterizing other sources of information, such as a web portal or a home page.          lab or department          organization or institution          wide-area portal (links to external neuroscience web sites) resource availability access     open       Resource may be accessed freely on the web without any kind of sign-in.     open with registration       Resource access requires signing up for an account or entry of a password, or resource is offline and contact information is required. However any person may access the resource.     restricted/private       Resource access is granted only to certain parties or members of a particular organization.     unknown/mixed       Availability is unknown or does not fall under any of the other categories. Return To Top method     HTML web pages       Resource is browsed and accessed through plain HTML web pages and/or downloads.     dynamic web pages (Javascript, Applets, etc)       Resource is browsed and accessed through a web browser-based interface that possesses some of the dynamic / interactive characteristics of an ordinary application.     software client       Resource is browsed and accessed through a software application that runs on a user's local machine, without a web browser.     web service       Resource may be accessed over the internet by software using specific protocols for remote procedure calls.     offline       Resource is offline.     unknown       Access method unknown. (Usually this is set in entries that have been imported from another catalog that does not contain this information. This entry should be edited to change this to the correct value.) Return To Top license     no license       The resource's contents may be used without any restriction or need to acknowledge the source.     acknowledgement required       The resource and/or content contributors should be acknowledged when its contents are used.     open source software       The resource includes open source software.          GPL style            The resource is open source and uses a license similar to the GNU Public License that requires all derivative works to be open source.          LGPL, Mozilla style            The resource is open source and uses a license similar to the Lesser GNU Public License that requires its own source code to be distributed with any derivative works.          BSD, MIT, Apache style            The resource is open source and carries no restrictions on derivative works.     closed source software       The resource includes closed source software.          commercial            Commercial software license.     other restriction       Use of the resource's contents is restricted in a way not covered by any of the other categories. Return To Top terminology     none       None.     public/open/shared       Resource employs, for data description, representation, or indexing, a terminology that can be used by other resources.          community standard            Resource employs, for data description, representation, or indexing, a terminology that can be used by other resources. However the terminology is closed to modification or expansion by people or organizations besides the originators.     private/local/customized       Resource employs, for data description, representation, or indexing, a terminology that cannot, should not, or was not intended to be used by other resources. Return To Top coverage     definitive / gold standard       Resource is the definitive source for data of the type it contains.     significant       Resource has a significant collection of data in its domain.     promising       Resource's contents are growing. data type     molecular/genetic          sequence              genetic/DNA/RNA              protein          structure          concentration/flux/activity              pH          expression          molecular interaction              reaction kinetic/thermodynamics     neurobiological          ultrastructure          structure/architecture              connectivity/circuitry              map              section              vasculature              dynamic metrics          function              electrophysiological activity/signaling                  action potentials                  synaptic potentials                  field potential                  EEG [electroencephalogram]              functional-imaged activity     body structure     behavior/performance          cognition/learning/memory          mechanical/motor activity              position/location              velocity/acceleration              force/tension/torque              pressure                  ocular                  intracranial/CSF [cerebrospinal fluid]          affect/emotion          autonomic/systemic metrics              cardiac/cardiovascular              respiration              GSR/skin resistance              temperature          sensory perception              audition              olfaction              somatic sensation              vision              pain/nociception     literature          abstract          citation          commentary          full text     metadata          ontology          terminology     model specification     analysis tools     simulation tools     materials neural structure structure / location     CNS [central nervous system]          brain              forebrain                  cerebral cortex                      frontal lobe/area                      parietal lobe/area                      temporal lobe/area                      occipital lobe/area                      limbic lobe/area                          hippocampus/hippocampal formation                  cerebral white matter                  basal ganglia                      striatum                      globus pallidus                      amygdala                  basal forebrain                  diencephalon                      thalamus                      hypothalamus/hypophysis              midbrain                  tectum                  tegmentum                  substantia nigra              hindbrain                  cerebellum                      cerebellar cortex                      cerebellar nuclei                  pons                  medulla          spinal cord              cervical              thoracic              lumbar              sacral     peripheral nervous system [PNS]          autonomic nervous system          cranial nerves          peripheral nerves          retina          cochlea          enteric nervous system Return To Top level_or_component     body     brain          connectivity/white matter/tract          region/nucleus          map/section     network/circuit/column     cell          glia          neuron     sub/transcellular component/compartment          axon          cytoskeleton          dendrite          intracellular traffic          membrane              channel/receptor          soma              nucleus              Golgi/trans-Golgi          synapse     molecule/gene          sequence          interaction/signaling pathway          structure Return To Top organism     human     invertebrate          annelid              leech          arthropod              crustacean                  crab                  lobster              insect                  cockroach                  cricket                  fly                      Drosophila m.                  honeybee [Apis m.]          mollusc              gastropod                  Aplysia c.              squid          nematode              C. elegans     nonhuman vertebrate          avian              chicken          fish              zebrafish          mammal              cat              primate (nonhuman)                  baboon                  monkey                      macaque [Macaca sp.]                      capuchin [Cebus sp.]                      squirrel monkey [Saimiri sp.]                      owl monkey [Aotus sp.]                      marmoset [Callithrix sp.]              rabbit              rodent                  mouse                      c57bl/6j                      dba/2j                      cross                  rat              sheep technique     chemical          CD          micro/calorimetry          gel/electrophoresis          HPLC/chromatography [high-pressure liquid chromatography]          mass spectroscopy          microdialysis          NMR [nuclear magnetic resonance]          radioassay          Xray crystallography     computed tomography/imaging          CAT [computer axial tomography]          MRI [magnetic resonance imaging]              structural              functional              spectrographic          PET [positron emission tomography]          SPECT [single photon emission computed tomography]     electrode-based          extracellular              single electrode              multiple electrode          intracellular/whole-cell/clamp              voltage-clamp              patch          amperometric              pH              ion sensitive (non-H ion)          macroelectrode              cuff/suction              field/surface                  EEG [electroencephalography]     electron microscopy [EM]          SEM [scanning electron microscopy]          TEM [transmission electron microscopy]          STEM [scanning transmission electron microscopy]     genomics/proteomics          expression chip/microarray          in situ hybridization          sequence     histology          staining              golgi              immunocytochemistry              immunohistochemistry              myelin              nissl          radiolabeling     light microscopy/optical imaging          bright field          dark field          intrinsic          fluorescence/chemiluminescence/phosphorescence              multi-photon              confocal              FRET [fluorescence resonance energy transfer]          Nomarski/DIC [differential interference contrast]          phase          polarization          spectroscopy          TIRM [total internal reflection microscopy]     MEG [magnetoencephalography]     mechanical sensors          sound pressure level detectors     physiological monitors          EKG [electrocardiograph]          polygraph/poysomnograph          spirometer/respirometer          thermal monitors     reports/narratives          clinical reports          subject reports     videography and photography     analytic tools     modeling/simulation tools     signal processing tools     visualization tools functional context neurobiological_focus     autonomic nervous system function     cognition          learning/memory     emotion     motor/action          locomotion          oculomotor function     sensation          audition          chemical sensation              olfaction              taste/gustatory sensation          somatosensation              proprioception              touch/tactile sensation              pain/nociception              visceral sensation          vision     sleep Return To Top stage     embryological stage (prenatal)     developmental stage (postnatal)     adult     aging          degenerative Return To Top disease     degenerative disease/dementia          Alzheimer/SDAT [senile dementia of Alzheimer type]          ataxias          diffuse Lewy body disease          dyskinesias/palsies          Huntingtons disease          motor degenerative disease              ALS [amyotrophic lateral sclerosis]              spinal muscular atrophy [SMA]          multiple system atrophy          Parkinsons disease          prion disease              CJD [Creutzfeld-Jacob disease, inc. variant]          progressive supranuclear palsy          sensorimotor degenerative disease     demyelinating diseases          MS [multiple sclerosis]          polyneuropathy     developmental disease     disorders of consciousness          minimally conscious state          persistent vegetative state          coma     epilepsy          partial/focal seizures              simple partial seizures              complex partial seizures          primary generalized              tonic/tonic-clonic seizures              absence epilepsy              myoclonic seizures              atonic seizures          status epilepticus     infectious nervous system disease          bacterial infection of the nervous system          viral infection of the nervous system     metabolic/nutritional disease     myopathy     neuromuscular disease          myasthenia gravis [MG]          Lambert-Eaton myasthenic syndrome [LEMS]     neoplastic disease          primary neoplastic disease              glioma              meningioma          metastatic disease of the nervous system          paraneoplastic disorder     psychiatric/mental health disorders          anxiety disorder          autism          depressive disorder          bipolar disorder          drug abuse              alcohol abuse              cannabinoid abuse              cocaine abuse              nicotine abuse              opiate abuse          psychosis          schizophrenia     stroke/cerebrovascular disease          hemorrhagic stroke          ischemic stroke     trauma (to the nervous system) Return To Top