Summary Database (Preliminary Version)
Dear all,
Mihail and I decided to go through the following phases to solve the task Dr. Arbib had proposed us to do:
Phase 1) Analyze Amanda's SDB schema and come up with our own schema that would preserve some of her ideas and at the same time represent our ideas of how the SDB should be structured. As you may have noticed, Amanda's schema has all the bibliographical information mixed with the neuronatomical information, which makes her schema difficult to read. Besides, as we discussed, the neurotransmitter and cell tables are very detailed. In the schema we propose, all this detailed info is seen as belonging to a clump of information (actually Amanda and Jeff have some neat ideas in how to place all this information into clumps and then allowing search by defining keywords).
Phase 2) Populate the new schema with data extracted from Mike Crowley's thesis and from the neuranatomical database available through the WEB from Washington University. In doing so, we were at the same time validating our DB schema. For this reason, the schema depicted in the figure below actually reflects its second version, since phase 2 is currently underway.
Phase 3) Generate the SQL code for each table and create the tables in Illustra.
Phase 4) Populate the Illustra tables with data from sources other than the ones used in Phase 1. This also implies a new validation phase.
Phase 5) Validation of the
proposed schema in the form of queries.
Figure 1: SDB schema
Table "Neuronatomical_Info" is the super-table that defines the fields "Name", "Species", "Description", and "Bib_References". These fields are inherited by the tables "Cell", "Structure", and "Connections", which are foreseen as the core tables of the schema proposed herein.
In Figure 1, the fields "Description", "Morphological_Charac", and "Physiological_Param" are to be viewed as clumps/beads of data (see Ilya's e-mail for more information on Clumps/Beads).
In the table "Cell", the field "Morphological_Charac" incorporates cell characteristics such as the shape, dimension of the soma, myielination, etc.; while the field "Physiological_Param" incorporates features such as membrane potential, threshold, firing rate, type of neurotransmitter, time constant, etc. It is worth mentioning that these fields are to be seen as clumps of data, in which the relevant information could be searched by the use of keywords. We also want to point out that the information contained in Crowley's thesis is not sufficient to fill out the tables. In this way, new data from other sources have to be looked at (see Phase 4 above).
As presented by Amanda in our meeting last week, the schema has to contain a link to a homology engine. We foreseen this to be linked to our "Neuroanatomical_Info" table. A neuroanatomical dictionary would be useful, for example, for the field "Description" which appears in table "Structure". The field "Description" in that table is understood as incorporating the definition of the particular anatomical structure in terms of position, ontogenetical origin, etc. Besides, if available, a functional decription could be provided. An example of such a dictionary an be found at http://rprcsgi.rprc.washington.edu/~joev, which gives the different definitions of brain structures for monkey and human, according to specific neuroanatomical atlases.
Table "Technique" was created to represent the techniques used to reveal connections and/or cells. These would include cases of anteriograde and/or retrograde stainning, etc.
Table "Experiments" was created in a way to represent the important features of a particular experiment that is relevant for a particular structure or cell. For example, in Crowley's thesis, particular aspects of experiments described in the literature were used to highlight the functional aspects of structures/cells that were important for the fundamentation of the proposed models. We assume that the whole experiment (methods, results, and discussion) would actually be part of the article repository database and the reference would be part of the bibliography database. This assumption is represented by the Bib_References field.
Finally, table "Connections" contains references to input and output structures, besides the main structure it is associated with.
Below, please find some of the tables we have been populating as part of what was described in Phase 2 above. Please, e-mail us your comments/critiques as soon as possible so that we can incorporate your suggestions into our design before the next BMW meeting.
Alex & Mihail
The following tables can be find below:
Structure
Basal Ganglia
Caudate Nucleus
Supperior Colliculus (Mike's Thesis)
Supperior Colliculus (Washington U. site)
Cell
interneuron
long-lead burst neuron
tonic neuron
projection neuron
Neurons from the superficial layer of Superior colliculus
long-lead burst neurons
Connections
Structure: Neostriatum
Structure: Striatum
Structure: Superior Colliculus
Experiment
Superior Colliculus - Single-Unit Recordings
Superior Colliculus - Lesion Studies
Name: Basal Ganglia
Species: Homo Sapiens
Description: The term basal ganglia (Crosby) refers to a portion of subcortical telencephalon which includes in addition to the basal ganglia as defined in NeuroNames (corpus striatum and amygdaloid nuclear complex) the claustrum, nucleus subputaminalis and substantia innominata. (Wahington U site)
Bib_References:
Crosby, E.C., Humphrey, T. and Lauer, E.W., CORRELATIVE ANATOMY OF THE NERVOUS SYSTEM, The MacMillan Co., New York, N.Y., 1962
Location:
Has_Structures:
caudate nucleus,
putamen,
globus pallidus,
subthalamic nucleus,
substantia nigra
Name: Caudate Nucleus
Species: Homo Sapiens
Description: none available...
Bib_References:
Carpenter, M.B. and Sutin, J., HUMAN NEUROANATOMY, Williams and Wilkins Co., Baltimore, Maryland, 1983.
Location:
Has_Structures:
head of caudate nucleus,
body of caudate nucleus,
tail of caudate nucleus
Name: interneuron
Species: Rat
Structure: Basal Ganglia, Neostriatum
Description: Wilson, Chang et al. (1990) found that the tonically active giant aspiny interneurons fire with a frequency less than 20 Hz.(pg.101)
Morphological_Charac: aspiny, giant
Physiological_Param: fire rate with a frequency less than 20 Hz
Bib_References:
Wilson, C. J., H. T. Chang, et al. (1990). "Firing pattern and synaptic potentials of identified giant aspiny interneurons in the rat neostriatum." Journal of Neuroscience 10(2): 508-519.
Name: long-lead burst neuron
Species: Not specified
Structure: Brainstem
Description: Long-lead burst neurons receive direct excitatory connections from the frontal eye fields and the superior colliculus. These neurons discharge at a high frequency just before and during saccades of the ipsilateral eye. They project to medium-lead burst neurons that make direct excitatory connections to motor neurons.(pg 74)
Morphological_Charac: Not specified
Physiological_Param: Not specified...or: high frequency discharge before and during saccades of the ipsilateral eye.
Bib_References: Not specified
Name: tonic neuron
Species: Not specified
Structure: Brainstem
Description:
Tonic neurons maintain the position of the eye. They fire at a steady rate when the eye is not moving and increase, or decrease, their firing rate when the eye is moved to a new position depending on the eccentricity of the eye. (pg 74)
Tonic neurons and inhibitory burst neurons are required to maintain eye position through the ocular muscles and to release opposing muscles to allow the eye to move in a particular direction, respectively. (pg 74)
Morphological_Charac: Not specified
Physiological_Param: They fire at a steady rate when the eye is not moving and increase, or decrease, their firing rate when the eye is moved to a new position depending on the eccentricity of the eye.
Bib_References: Not Specified.
Name: projection neuron
Species: Rat
Structure: Basal Ganglia, Neostriatum
Description: Wilson et al. (1981) found that the GABAergic inhibitory projection neurons in the BG rarely fire more than 40 spikes per second, which is the maximum firing rate for our model neurons. (pg.101)
Morphological_Charac: spiny
Physiological_Param: inhibitory maximal fire rate is 40 spikes per second. Neurotransmitter GABA
Bib_References:
Wilson, C. J. and P. M. Groves (1981). "Spontaneous firing patterns of identified spiny neurons in the rat neostriatum." Brain Research 220: 67-80.
Name:
Structure: Neostriatum
Species: Primates Squirrel Monkey
Input_Structure: Cerebral Cortex
Output_Structure: Frontal Cortex
Type: excitatory/inhibitory
Description: The neostriatum receives nearly all of the input to the basal ganglia, receiving topographically organized afferents from all four lobes of the cerebral cortex, including sensory, motor, association, and limbic areas (Alexander, DeLong et al. 1986; Alexander, Crutcher et al. 1990; Gerfen 1992; Parent and Hazrati 1993). However, it projects back only to frontal cortex, through the thalamus.(pg. 94)
Technique:
Bib_References:
Alexander, G. E., M. R. DeLong, et al. (1986). "Parallel organization of functionally segregated circuits linking basal ganglia and cortex." Ann Rev Neurosci 9: 357-381.
Alexander, G. E., M. R. Crutcher, et al. (1990). "Basal ganglia-thalamocortical circuits: Parallel substrates for motor, oculomotor, "prefrontal" and "limbic" functions." Prog. Brain Res. 85: 119-146.
Gerfen, C. R. (1992). "The neostriatal mosaic: Multiple levels of compartmental organization in the basal ganglia." Ann. Rev. Neurosci. 15: 285-320.
Parent, A. and L.-N. Hazrati (1993). "Anatomical aspects of information processing in primate basal ganglia." TINS 16(3): 111-116.
Name:
Structure: Striatum
Species: Primates
Input_Structures: Frontal Eye Field, Supplementary Eye Field
Output_Structures: External Globus Pallidus, Substantia Nigra Pars Reticulata, Internal Globus Pallidus
Type: excitatory/inhibitory
Description: The striatum projects to its output nuclei (substantia nigra pars reticulata and internal globus pallidus)via a direct and indirect path. The indirect path includes the GPe and STN and excites the BG output nuclei, whereas the direct path contains GABA neurons which inhibit the tonically firing SNr neurons. (pg. 94)
Technique:
Bib_References:
Connection Alexander, G. E., M. R. Crutcher, et al. (1990). "Basal ganglia-thalamocortical circuits: Parallel substrates for motor, oculomotor, "prefrontal" and "limbic" functions." Prog. Brain Res. 85: 119-146.
Structure: Superior Colliculus
Cell: Neurons from intermediate layers
Type: Single-unit recordings
Description: Recordings from awake animals reveal that the majority of neurons in the intermediate layers fire before contralateral saccades of specific size and direction (Schiller and Stryker 1972; Wurtz and Goldberg 1972; Sparks and Mays 1980; Sparks 1986). (pg. 62)
Bib_References:
Schiller, P. H. and M. Stryker (1972). "Single-unit recording and stimulation in superior colliculus of the alert rhesus monkey." J. Neurophysiol. 35: 915-924.
Wurtz, R. H. and M. E. Goldberg (1972). "Activity of superior colliculus in behaving monkey. III. Cells discharging before eye movements." J. Neurophysiol. 35: 575-586.
Sparks, D. L. and L. E. Mays (1980). "Movement fields of saccade-related burst neurons in the monkey superior colliculus." Brain Res. 190: 39-50.
Sparks, D. L. (1986). "Translation of sensory signals into commands for control of saccadic eye movements: Role of primate superior colliculus." Physiol. Rev. 66: 118-171.
Structure: Superior Colliculus
Cell: Not Specified
Type: Lesion Study
Description: Lesions of a small part of the colliculus transiently affect the latency, accuracy, and velocity of saccades, lesions of the entire SC transiently render a monkey unable to make any contralateral saccades, but this quickly recovers. The monkey at first makes saccades that are slower, less accurate, and have a longer reaction time than before the lesion, but ultimately even these recover almost entirely. (pg 63)
Bib_References: None Specified
Name: Superior Colliculus
Species: Primate
Description: The superior colliculus can be divided into two sets of layers (Sparks 1986; Moschovakis et al. 1988): the superficial layers and the intermediate and deep layers.(pg. 61)
Bib_References:
Sparks, D. L. (1986). "Translation of sensory signals into commands for control of saccadic eye movements: Role of primate superior colliculus." Physiol. Rev. 66: 118-171.
Location:
Has_Structures:
the superficial layers
the intermediate and deep layers
Name: Superior Colliculus
Species: Homo Sapiens, Primates
Description: "...tectum that consists of the paired superior colliculi and inferior colliculi." - Washington U. site
Bib_References: Not Specified
Location: Midbrain
Has_Structures:
zonal layer of superior colliculus
superficial gray layer of superior colliculus
superficial white layer of superior colliculus
Name:
Structure: Superior Colliculus
Species: Primates
Input_Structure:
Retina
Prestriate cortex
Middle temporal cortex
Parietal cortex (LIP)
Frontal eye fields (FEF)
Output_Structure:
Thalamic medial pulvinar nucleus
Thalamic lateral posterioris nucleus
Brainstem
Type: excitatory (?)
Description:
The superficial layers of SC receive both direct input from the retina and a projection from striate cortex for the entire contralateral visual hemifield. (pg 61)
Cells in the two intermediate and deep layers of SC are primarily related to the oculomotor system. These cells receive visual inputs from prestriate, middle temporal, and parietal cortices, and motor input from FEF. (pg 61)
This motor output drives the LLBN cells of the paramedian pontine reticular formation (PPRF), in the brainstem, that specify how far the eye should move. (pg. 62)
In fact, neurons in the superficial layers do not project directly to the intermediate layers. Instead, they send their fibers to the medial pulvinar (Asanuma, Andersen et al. 1985) and lateral posterior nuclei of the thalamus; from there the signals are routed to cortical areas and back to the intermediate layers of the SC. (pg 63)
Technique: Not Specified
Bib_References:
Asanuma, C., Andersen, R. A., et al. (1985). "The thalamic relations of the caudal inferior parietal lobule and the lateral prefrontal cortex in monkeys: Divergent cortical projections from cell clusters in the medial pulvinar nucleus." J. Comp. Neurol. 241: 357-381.
Sparks, D. L. (1986). "Translation of sensory signals into commands for control of saccadic eye movements: Role of primate superior colliculus." Physiol. Rev. 66: 118-171.
Moschovakis, A. K., A. B. Karabelas, et al. (1988). "Structure-function relationships in the primate superior colliculus. I. Morphological classification of efferent neurons." J. Neurophysiol. 60: 232-262.
Name: Neurons from the superficial layer of Superior colliculus
Species: Primates
Structure: Superior colliculus
Description:
Neurons in the superficial SC have specific visual receptive fields: Half of the neurons have a higher frequency discharge in response to a visual stimulus when a monkey is going to make a saccade to that stimulus [Goldberg, 1972; Wurtz, 1976]. If the monkey attends to the stimulus without making a saccade to it, for example by making a hand movement in response to a brightness change, these neurons do not give an enhanced response.(pg. 61)
In each of the two sets of layers in SC - superficial and deep - activity can occur independently of the other (Goldberg, Eggers et al. 1991). Thus, sensory activity in the superficial layers need not lead to motor output from the intermediate layers, and output can occur without sensory activity in the superficial layers. In fact, neurons in the superficial layers do not project directly to the intermediate layers. (pg. 63)
Morphological_Charac: Not Specified
Physiological_Param:
specific visual receptive fields
half of neurons have a higher frequency discharge in response to a visual stimulus when a monkey is going to make a saccade to that stimulus
Bib_References:
Wurtz, R. H. and M. E. Goldberg (1972). "Activity of superior colliculus in behaving monkey. III. Cells discharging before eye movements." J. Neurophysiol. 35: 575-586. (there is no match between the citation in the text, and bibliography).
Goldberg, M. E., H. M. Eggers, et al. (1991). The Ocular Motor System. Principles of Neural Science. E. R. Kandel, J. H. Schwartz and T. M. Jessell. New York, Elsevier: 660-678.
Name: long-lead burst cells
Species: Primates, Rhesus Monkey
Structure: Brainstem, Paramedian pontine reticular formation
Description
These cells have movement fields analogous to the receptive fields of sensory neurons. The movement field is that part of the visual field to which the eye moves in response to activity in the cell. Schiller (1980) and Stryker (1990) found that electrical stimulation of the SC evokes saccades into the movement field of the stimulated neurons. The movement fields are in register with the visual and auditory receptive fields, so that neurons that drive eye movements to a certain target are found in the same region as the cells excited by the sounds and image of that target. (pg. 61)
Morphological_Charac: Not specified
Physiological_Param:
movement fields analogous to the receptive fields of sensory neurons
electrical stimulation of the SC evokes saccades into the movement field of the stimulated neurons
movement fields are in register with the visual and auditory receptive fields
Bib_References:
Schiller, P. H. and S. D. True (1980). "Deficits in eye movements following frontal eye field and superior colliculus ablations." J. Neurophysiol. 44: 1175-1189.
Stryker, M. P., B. Chapman, et al. (1990). "Experimental and theoretical studies of the organization of afferents to single-orientation columns in visual cortex." Cold Springs Harbor Symp. Quant. Biol. 55: 515-527.
Goldberg, M. E., H. M. Eggers, et al. (1991). The Ocular Motor System. Principles of Neural Science. E. R. Kandel, J. H. Schwartz and T. M. Jessell. New York, Elsevier: 660-678.