************************************************************************** ** ** ** README for "White_Fig" directory (folder) ** ** ** ** ** ** CCeP (Cybernetic Caenorhabditis elegans Program), ** ** December 28, 2003. ** ** ** ************************************************************************** ================================= INTRODUCTION ================================= Files in this "White_Fig" directory (folder) describe the synaptic connectivity shown in the figures in the paper: White, J. G., Southgate, E., Thomson, J. N. and Brenner, S. (1986). "The structure of the nervous system of the nematode Caenorhabditis elegans", Phil. Trans. R. Soc. London B 314, pp.1-340. In that paper, authors have studied the somatic nervous system except that in the pharynx. ================================= FILES AND DIRECTORIES (FOLDERS) ================================= - [White_Fig] -----+- README_WF.txt +- NOTE_WF.pdf +- synapse_WF.txt +- process_WF.pdf | +- [neurons] --- XXX_WF.txt o README_WF.txt: This file. ASCII text file that gives general information on files in this "White_Fig" directory (folder). o NOTE_WF.pdf: PDF file that illustrates the format of data in detail. o synapse_WF.txt: ASCII text file in which all of the data files "XXX_WF.txt" in the "neurons" directory (folder) are included. For RMFL and RMFR neurons, however, only "RMFL_WF.txt" and "RMFR_WF.txt" (the N2U reconstruction) are included to make this file (see below for the reason). o process_WF.pdf: PDF file that illustrates the correspondence between the "process" (branched morphology of neuron) and the index of process (2nd column in the data files "synapse_WF.txt" and "XXX_WF.txt"). o XXX_WF.txt in the "neurons" directory (folder): ASCII text files that describe the synaptic connectivity shown in the figures in the original paper for each reference neuron. Here XXX denotes a name of reference neuron. In the original paper, RMF (RMFL/R) neurons are illustrated in two figures. One illustrates neurons in the N2U series (adult hermaphrodite), the other illustrates those in the JSH series (L4 larva). We provide in "RMFL_WF.txt" and "RMFR_WF.txt" the N2U reconstruction while the JSH reconstruction is provided in "RMFL_JSH_WF.txt" and "RMFR_JSH_WF.txt". ================================= FORMAT OF DATA ================================= To exactly list the synaptic connectivity shown in the figures in the original paper, we describe a synapse by the eight items which represent the followings. (1) name of reference neuron (2) the (branching) process of neuron (3) location of a synaptic contact (a dot or a bar "|" illustrated in the original paper) on the process (4) which symbol of synapse type is attached to a synaptic contact? (5) a type of synaptic contact (6) name of partner neuron (7) whether a synapse is multiple or not? (8) comment on an ambiguous or questionable synaptic contact Corresponding to the eight items, the data files "synapse_WF.txt" and "XXX_WF.txt" consist of eight columns such as in the following table. Table. Example of record in the database. ------------------------------------------------- column 1 2 3 4 5 6 7 8 ------------------------------------------------- ADAL A 9 9 G AVDR - - ADAL A 10 10 S AVBR - - ADAL A 11 11 R AIAL * - ------------------------------------------------- [1st column] Name of reference neuron [2nd column] Index of process: Each process of neuron is labeled with an alphabet. When a neuron has branched precesses, a process at the upper left-hand side of the original figure is given priority in assignment of the index. Since the index is assigned to the process without a synaptic contact, the index does not always begin from the alphabet ``A'' in the database. Refer to the PDF file "process_WF.pdf" for the correspondence between the present index and the process illustrated in the original paper. [3rd column] Serial number of synaptic contact: All the synaptic contacts (illustrated with a dot or a bar "|" in the original figures) on the process are numbered. Consecutive numbers are used in a given reference neuron. From a combination of the 2nd column (the index of process) and the 3rd column (the present number), location of contacts on the process is known up to topology. Refer to "NOTE_WF.pdf" for how to number the synaptic contact. [4th column] Serial number of synapse symbol: All the symbols of synapse type (arrows and T lines in the original figures) are numbered. Consecutive numbers are used in a given reference neuron. Refer to "NOTE_WF.pdf" for how to number the symbol of synapse type. [5th column] Index of synapse type: Synapse type is illustrated with an arrow (a chemical synapse) or a T line (a gap junction) in the original figures. In the case of chemical synapse, furthermore, "send" or "receive" is distinguished by the direction of the arrow. We use four indices, "S", "R", "G" and "-" to describe the synapse type. "S": The reference neuron sends chemical synapse to its partner neuron. "R": The reference neuron receives chemical synapse from its partner neuron. "G": A gap junction connects the reference neuron with its partner neuron. "-": A symbol of synapse type is missing. [6th column] Name of partner neuron listed in "name_neurons.txt" or others listed in "name_others.txt". [7th column] Index to indicate that an asterisk is attached to the partner neuron: When a reference neuron receives multiple chemical synapses, only one of its presynaptic partner neurons is explicitly written with an asterisk "*" in the original figures. We use two indices, "*" and "-". In the case of chemical synapse, therefore, multiple chemical synapses are distinguished from a single chemical synapse by this index. In the case of gap junction, the index should be "-". "*": An asterisk is attached to the name of partner neuron. "-": No asterisk is attached to the name of partner neuron. [8th column] Comment index: When descriptions in the original figures are questionable, we have commented in this column. We have classified the comments into 33 types, and distinguish them by the following indices. Indices "wf1-5" are due to deviations from the rules of the original paper. "-": Nothing to comment. "wf1": This is a presynaptic chemical synapse ("Send"), but an asterisk is attached to the partner neuron in the original paper against its rule. "wf2": This is a postsynaptic chemical synapse ("Receive") with two or more names of partner neurons. This may mean a multiple receive synapse. "wf3": This is a gap junction, but multiple names of partner neurons are written in the original paper against its rule. "wf4": This is a gap junction, but an asterisk is attached to the partner neuron in the original paper against its rule. "wf5": This is a gap junction between "*L" and "*R" neurons in the same class. In the figure, the names of the two neurons are denoted for the identical symbol of synapse type which is common to the two neurons. The database of each neuron has two lines for this connection, however, it means a gap junction between contralateral neurons in the same neuron class. "wf6": This is a gap junction between processes within the same neuron. "wf7": No symbol of synapse type is attached in the original paper. "wf8": No symbol of synapse type is attached in the original paper, but the synaptic contact is illustrated with a bar "|" that often represents a gap junction. "wf9": The symbol of synapse type is illustrated with a left-right arrow. "wf10": Multiple symbols of synapse types are corresponding to an identical synaptic contact. "wf11": "wf10" and "wf3". "wf12": "wf10" and "wf7". "wf13": Comment peculiar to RIPL. Boundary between RIPL and RIPR is not clear in the original figure. It is possible that the synapse lies on the process E of RIPR. "wf14": Comment peculiar to RIBR. A symbol of this synaptic contact is drawn over the boundary of two neurons. It is possible that the synapse lies on the process F of RIBL (or RIBR). "wf15": Comment peculiar to RIBL. From the same reason as above, it is possible that the synapse lies on the process F of RIBR (or RIBL). "wf16": Comment peculiar to SMBVL. Location of the synaptic contact is erroneous. It is possible that index in column 5 is "R". "wf17": The index of synapse type ("Send" or "Receive") is questionable because the guiding line is ended between the symbol of synapse type and the name of partner neuron in the original figure. "wf18": "wf2" and that the index of synapse type ("Send" or "Receive") is questionable because the guiding line is ended at the end of the name of partner neuron in the original figure. "wf19": The guiding line does not clearly point to the synaptic contact in the original figure. "wf20": "wf19" and "wf5". "wf21": The name of partner neuron is not clearly printed in the original figure. "wf22": The asterisk is not clearly printed in the original figure. "wf23": This synapse might be NMJ which is a special cases of chemical synapses, however, the symbol of synapse type is illustrated with that for "Gap junction". "wf24": Comment peculiar to RMDR. The name of partner neuron "SVPL" does not exist. It should be read "PVPL" or other names of neurons. "wf25": Comment peculiar to RMGL. The name of partner neuron "RMVDL" does not exist. It should be read "RMDVL" or other names of neurons. "wf26": When distances of the several synaptic contacts from the soma seem to be the same, the left (leftmost) synaptic contact is assigned the smaller (smallest) serial number. "wf27": The serial number of synaptic contact is not definitive, because distances from the soma are not distinguishable due to gap junctions usually marked with a bar "|" along process. "wf28": "wf27" and "wf2". "wf29": "wf27" and "wf3". "wf30": "wf27" and "wf10". "wf31": The N2U reconstruction of RMF (RMFL/R) neurons. The data is included in "synapse_WF.txt". "wf32": The JSH reconstruction of RMF (RMFL/R) neurons. The data is not included in "synapse_WF.txt". "wf33": "wf32" and "wf21". ================================= DETAILED INFORMATION ================================= Refer to "NOTE_WF.pdf" for more detailed information on the format of data. Example of the record in the database is also shown in "NOTE_WF.pdf".