{"action":"created","issue":{"url":"https://api.github.com/repos/metabolite-atlas/metatlas/issues/32","labels_url":"https://api.github.com/repos/metabolite-atlas/metatlas/issues/32/labels{/name}","comments_url":"https://api.github.com/repos/metabolite-atlas/metatlas/issues/32/comments","events_url":"https://api.github.com/repos/metabolite-atlas/metatlas/issues/32/events","html_url":"https://github.com/metabolite-atlas/metatlas/issues/32","id":109862608,"number":32,"title":"Add Scan Parameters Information","user":{"login":"benbowen","id":810953,"avatar_url":"https://avatars.githubusercontent.com/u/810953?v=3","gravatar_id":"","url":"https://api.github.com/users/benbowen","html_url":"https://github.com/benbowen","followers_url":"https://api.github.com/users/benbowen/followers","following_url":"https://api.github.com/users/benbowen/following{/other_user}","gists_url":"https://api.github.com/users/benbowen/gists{/gist_id}","starred_url":"https://api.github.com/users/benbowen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/benbowen/subscriptions","organizations_url":"https://api.github.com/users/benbowen/orgs","repos_url":"https://api.github.com/users/benbowen/repos","events_url":"https://api.github.com/users/benbowen/events{/privacy}","received_events_url":"https://api.github.com/users/benbowen/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/metabolite-atlas/metatlas/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":10,"created_at":"2015-10-05T18:55:27Z","updated_at":"2015-11-02T14:46:16Z","closed_at":null,"body":"Currently, we would have to dive into the mzML file to get the metadata about a scan.  Its in the header of the xml file.  Not all vendors store the information in the same format.\r\n\r\nNevertheless, we need a minimal but sufficient specification to store this.  Around 10K scans per file.  \r\nOne way is here:\r\nhttps://www.draw.io/#G0BweRoDuGcsLBOGVvUlFneUNGdDg"},"comment":{"url":"https://api.github.com/repos/metabolite-atlas/metatlas/issues/comments/153037841","html_url":"https://github.com/metabolite-atlas/metatlas/issues/32#issuecomment-153037841","issue_url":"https://api.github.com/repos/metabolite-atlas/metatlas/issues/32","id":153037841,"user":{"login":"benbowen","id":810953,"avatar_url":"https://avatars.githubusercontent.com/u/810953?v=3","gravatar_id":"","url":"https://api.github.com/users/benbowen","html_url":"https://github.com/benbowen","followers_url":"https://api.github.com/users/benbowen/followers","following_url":"https://api.github.com/users/benbowen/following{/other_user}","gists_url":"https://api.github.com/users/benbowen/gists{/gist_id}","starred_url":"https://api.github.com/users/benbowen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/benbowen/subscriptions","organizations_url":"https://api.github.com/users/benbowen/orgs","repos_url":"https://api.github.com/users/benbowen/repos","events_url":"https://api.github.com/users/benbowen/events{/privacy}","received_events_url":"https://api.github.com/users/benbowen/received_events","type":"User","site_admin":false},"created_at":"2015-11-02T14:46:16Z","updated_at":"2015-11-02T14:46:16Z","body":"GetData and GetSpectrum would operate on SpectrumData, but GetChromatogram\nwould operate on ChroamtogramData.\n\nPerhaps the MSMS queries confound this, but it seems possible that for pos,\nneg, MS1, and MS2 layers, there could be both a spectrumdata and a\nchromatogram data.  The file api would use the correct logic to request\ndata.\n\nOn Mon, Nov 2, 2015 at 6:28 AM, Benjamin Bowen <bpbowen@lbl.gov> wrote:\n\n> Also, add ChromatogramData():\n>     mz ....\n>     i ....\n>     scan ....\n>\n> ChromatogramData would be lined up for a logically reduced set of mz\n> values to allow rapid slicing in the time dimension.  Currently, slicing is\n> fast for spectra and much slower for time.\n>\n>\n>\n> On Sun, Nov 1, 2015 at 8:26 AM, Steven Silvester <notifications@github.com\n> > wrote:\n>\n>> What if we organized the HDF file as such:\n>>\n>> class SpectrumData(tables.IsDescription):\n>>     mz = tables.Float32Col(pos=0)\n>>     i = tables.Float32Col(pos=1)\n>>     scan = tables.Int32Col(pos=2)\n>>\n>> class ScanParams(tables.IsDescription):\n>>     rt = tables.Float32Col(pos=0)\n>>     mz_range = tables.Float32Col(pos=0)\n>>     instrument = tables.StringCol(256, pos=1)\n>>     ion_source = tables.StringCol(256, pos=2)\n>>     mass_analyzer = tables.StringCol(256, pos=3)\n>>     polarity = tables.EnumCol(pos=4)\n>>     scan_duration = tables.Float32Col(pos=5)\n>>\n>> class MS2Params(ScanParams):\n>>     precursor_MZ = tables.Float32Col(pos=6)\n>>     precursor_intensity = tables.Float32Col(pos=7)\n>>     collision_energy = tables.Float32Col(pos=8)\n>>     fragmentation_type = tables.StringCol(256, pos=9)\n>>\n>> —\n>> Reply to this email directly or view it on GitHub\n>> <https://github.com/metabolite-atlas/metatlas/issues/32#issuecomment-152841728>\n>> .\n>>\n>\n>\n"}}