From 9c722132d4ce8dd2e6051386192bf581cd29792d Mon Sep 17 00:00:00 2001 From: Stephen Larson Date: Fri, 18 Dec 2015 10:37:32 -0800 Subject: [PATCH] update data sources to address #177 --- docs/data_sources.rst | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/docs/data_sources.rst b/docs/data_sources.rst index ff9e4d927..d63fd2397 100644 --- a/docs/data_sources.rst +++ b/docs/data_sources.rst @@ -22,27 +22,27 @@ in a superscript, and the decisions made during the curation process Neurons ------- -- Cell descriptions [1]_: Extracted from WormAtlas.org. Staged in [this tsv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/C.%20elegans%20Cell%20List%20-%20WormAtlas.tsv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L68) -- Lineage names [1]_: Extracted from WormAtlas.org. Staged in [this tsv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/C.%20elegans%20Cell%20List%20-%20WormAtlas.tsv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L68) -- Neuron names [2]_: Extracted from WormBase. Staged in [this csv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/C.%20elegans%20Cell%20List%20-%20WormBase.csv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L145) +- Neuron names [2]_: Extracted from WormBase. Dynamic version on [this google spreadsheet](https://docs.google.com/spreadsheets/d/1NDx9LRF_B2phR5w4HlEtxJzxx1ZIPT2gA0ZmNmozjos/edit#gid=1). Staged in [this csv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/C.%20elegans%20Cell%20List%20-%20WormBase.csv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L145) - Neuron types [1]_: Extracted from WormAtlas.org. Staged in [this csv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/Modified%20celegans%20db%20dump.csv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L287) -- Neurotransmitters [1]_: Extracted from WormAtlas.org. Staged in [this csv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/Modified%20celegans%20db%20dump.csv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L262) -- Neuropeptides [1]_: Extracted from WormAtlas.org. Staged in [this csv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/Modified%20celegans%20db%20dump.csv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L274) -- Innexins [1]_: Extracted from WormAtlas.org. Staged in [this csv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/Modified%20celegans%20db%20dump.csv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L268) +- Cell descriptions [1]_: Extracted from WormAtlas.org. Staged in [this tsv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/C.%20elegans%20Cell%20List%20-%20WormAtlas.tsv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L68) +- Lineage names [1]_: Extracted from WormAtlas.org. Dynamic version on [this google spreadsheet](https://docs.google.com/spreadsheets/d/1Jc9pOJAce8DdcgkTgkUXafhsBQdrer2Y47zrHsxlqWg/edit). Staged in [this tsv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/C.%20elegans%20Cell%20List%20-%20WormAtlas.tsv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L68) +- Neurotransmitters [1]_: Extracted from WormAtlas.org. Dynamic version on [this google spreadsheet](https://docs.google.com/spreadsheets/d/1Jc9pOJAce8DdcgkTgkUXafhsBQdrer2Y47zrHsxlqWg/edit). Staged in [this csv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/Modified%20celegans%20db%20dump.csv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L262) +- Neuropeptides [1]_: Extracted from WormAtlas.org. Dynamic version on [this google spreadsheet](https://docs.google.com/spreadsheets/d/1Jc9pOJAce8DdcgkTgkUXafhsBQdrer2Y47zrHsxlqWg/edit). Staged in [this csv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/Modified%20celegans%20db%20dump.csv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L274) +- Innexins [1]_: Extracted from WormAtlas.org. Dynamic version on [this google spreadsheet](https://docs.google.com/spreadsheets/d/1Jc9pOJAce8DdcgkTgkUXafhsBQdrer2Y47zrHsxlqWg/edit). Staged in [this csv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/Modified%20celegans%20db%20dump.csv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L268) Muscle cells ------------ -- Cell descriptions [1]_: Extracted from WormAtlas.org. Staged in [this tsv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/C.%20elegans%20Cell%20List%20-%20WormAtlas.tsv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L68) -- Lineage names [1]_: Extracted from WormAtlas.org. Staged in [this tsv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/C.%20elegans%20Cell%20List%20-%20WormAtlas.tsv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L68) -- Muscle names [2]_: Extracted from WormBase. Staged in [this csv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/C.%20elegans%20Cell%20List%20-%20WormBase.csv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L44) +- Muscle names [2]_: Extracted from WormBase. Dynamic version on [this google spreadsheet](https://docs.google.com/spreadsheets/d/1NDx9LRF_B2phR5w4HlEtxJzxx1ZIPT2gA0ZmNmozjos/edit#gid=1). Staged in [this csv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/C.%20elegans%20Cell%20List%20-%20WormBase.csv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L44) +- Cell descriptions [1]_: Extracted from WormAtlas.org. Dynamic version on [this google spreadsheet](https://docs.google.com/spreadsheets/d/1Jc9pOJAce8DdcgkTgkUXafhsBQdrer2Y47zrHsxlqWg/edit). Staged in [this tsv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/C.%20elegans%20Cell%20List%20-%20WormAtlas.tsv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L68) +- Lineage names [1]_: Extracted from WormAtlas.org. Dynamic version on [this google spreadsheet](https://docs.google.com/spreadsheets/d/1Jc9pOJAce8DdcgkTgkUXafhsBQdrer2Y47zrHsxlqWg/edit). Staged in [this tsv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/C.%20elegans%20Cell%20List%20-%20WormAtlas.tsv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L68) - Neurons that innervate each muscle [3]_: Extracted from data personally communicated by S. Cook. Staged in [this csv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/herm_full_edgelist.csv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L432) Connectome ---------- -- Gap junctions [3]_: Extracted from data personally communicated by S. Cook. Staged in [this csv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/herm_full_edgelist.csv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L423) -- Synapses [3]_: Extracted from data personally communicated by S. Cook. Staged in [this csv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/herm_full_edgelist.csv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L423) +- Gap junctions between neurons [3]_: Extracted from data personally communicated by S. Cook. Staged in [this csv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/herm_full_edgelist.csv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L423) +- Synapses between neurons [3]_: Extracted from data personally communicated by S. Cook. Staged in [this csv file](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/aux_data/herm_full_edgelist.csv). Parsed by [this method](https://github.com/openworm/PyOpenWorm/blob/945f7172f0dff1d022ce0574f3c630ee53297386/OpenWormData/scripts/insert_worm.py#L423) Curation note ^^^^^^^^^^^^^