.. _data_sources: |pow| Data Sources ================== The sources of data for PyOpenWorm are stored in the `OpenWormData repository `_. A few :py:class:`DataTranslators <~PyOpenWorm.datasource.DataTranslator>` translate these data into common PyOpenWorm data sources. You can list these by running:: pow source list and you can show some of the properties of a data source by running:: pow source show $SOURCE_IDENTIFIER For instance, you can run the following to see the top-level data source, try:: pow source show http://openworm.org/data This will print out summary descriptions of the sources that contribute to the main data source. A Note on |pow| Data -------------------- Below, each major element of the worm's anatomy that |pow| stores data on is considered individually. The data being used is tagged by source in a superscript, and the decisions made during the curation process (if any) are described. Neurons ------- - Neuron names [2]_: Extracted from WormBase. Dynamic version on `this google spreadsheet `_. Staged in `this csv file `_. Parsed by `this method `_. - Neuron types [1]_: Extracted from WormAtlas.org. Staged in `this csv file `_. Parsed by `this method `_. - Cell descriptions [1]_: Extracted from WormAtlas.org. Staged in `this tsv file `_. Parsed by `this method `_. - Lineage names [1]_: Extracted from WormAtlas.org. Dynamic version on `this google spreadsheet `_. Staged in `this tsv file `_. Parsed by `this method `_. - Neurotransmitters [1]_: Extracted from WormAtlas.org. Dynamic version on `this google spreadsheet `_. Staged in `this csv file `_. Parsed by `this method `_. - Neuropeptides [1]_: Extracted from WormAtlas.org. Dynamic version on `this google spreadsheet `_. Staged in `this csv file `_. Parsed by `this method `_. - Receptors [1]_: Extracted from WormAtlas.org. Dynamic version on `this google spreadsheet `_. Staged in `this csv file `_. Parsed by `this method `_. - Innexins [1]_: Extracted from WormAtlas.org. Dynamic version on `this google spreadsheet `_. Staged in `this csv file `_. Parsed by `this method `_. .. _gs1: https://docs.google.com/spreadsheets/d/1NDx9LRF_B2phR5w4HlEtxJzxx1ZIPT2gA0ZmNmozjos/edit#gid=1 .. _gs2: https://docs.google.com/spreadsheets/d/1Jc9pOJAce8DdcgkTgkUXafhsBQdrer2Y47zrHsxlqWg/edit .. _m3: https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L145 .. _m4: https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L287 .. _m5: https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L68 .. _m7: https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L262 .. _m8: https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L274 .. _m9: https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L280 .. _m10: https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L268 .. _csv1: https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/Modified%20celegans%20db%20dump.csv .. _csv2: https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/C.%20elegans%20Cell%20List%20-%20WormBase.csv .. _tsv1: https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/C.%20elegans%20Cell%20List%20-%20WormAtlas.tsv Gene expression data below, additional to that extracted from WormAtlas concerning receptors, neuropeptides, neurotransmitters and innexins are parsed by `this method `_: - Monoamine secretors and receptors, neuropeptide secretors and receptors [4]_: Dynamic version on `this google spreadsheet `_. Staged in `this csv file `_. Muscle cells ------------ - Muscle names [2]_: Extracted from WormBase. Dynamic version on `this google spreadsheet `_. Staged in `this csv file `_. Parsed by `this method `_. - Cell descriptions [1]_: Extracted from WormAtlas.org. Dynamic version on `this google spreadsheet `_. Staged in `this tsv file `_. Parsed by `this method `_. - Lineage names [1]_: Extracted from WormAtlas.org. Dynamic version on `this google spreadsheet `_. Staged in `this tsv file `_. Parsed by `this method `_. - Neurons that innervate each muscle [3]_: Extracted from data personally communicated by S. Cook. Staged in `this csv file `_. Parsed by `this method `_. .. _csv3: https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/herm_full_edgelist.csv .. _m11: https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L44 .. _m12: https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L432 Connectome ---------- - Gap junctions between neurons [3]_: Extracted from data personally communicated by S. Cook. Staged in `this csv file `_. Parsed by `this method `_. - Synapses between neurons [3]_: Extracted from data personally communicated by S. Cook. Staged in `this csv file `_. Parsed by `this method `_. .. _m13: https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L423 Curation note ^^^^^^^^^^^^^ There was another source of *C. elegans* connectome data that was created by members of the OpenWorm project that has since been retired. The history of this spreadsheet is mostly contained in `this forum post `_ We decided to use the Emmons data set [3]_ as the authoritative source for connectome data, as it is the very latest version and updated version of the *C. elegans* connectome that we are familiar with. ---------- Data Source References ---------------------- .. [1] Altun, Z.F., Herndon, L.A., Wolkow, C.A., Crocker, C., Lints, R. and Hall, D. H. (2015). WormAtlas. Retrieved from http://www.wormatlas.org - `WormAtlas Complete Cell List `_ .. [2] - Harris, T. W., Antoshechkin, I., Bieri, T., Blasiar, D., Chan, J., Chen, W. J., … Sternberg, P. W. (2010). WormBase: a comprehensive resource for nematode research. Nucleic Acids Research, 38(Database issue), D463–7. http://doi.org/10.1093/nar/gkp952 - Lee, R. Y. N., & Sternberg, P. W. (2003). Building a cell and anatomy ontology of Caenorhabditis elegans. Comparative and Functional Genomics, 4(1), 121–6. http://doi.org/10.1002/cfg.248 .. [3] Emmons, S., Cook, S., Jarrell, T., Wang, Y., Yakolev, M., Nguyen, K., Hall, D. Whole-animal C. elegans connectomes. C. Elegans Meeting 2015 http://abstracts.genetics-gsa.org/cgi-bin/celegans15s/wsrch15.pl?author=emmons&sort=ptimes&sbutton=Detail&absno=155110844&sid=668862 .. [4] Bentley B., Branicky R., Barnes C. L., Chew Y. L., Yemini E., Bullmore E. T., Vertes P. E., Schafer W. R. (2016) The Multilayer Connectome of Caenorhabditis elegans. PLoS Comput Biol 12(12): e1005283. http://doi.org/10.1371/journal.pcbi.1005283