{"action":"created","issue":{"url":"https://api.github.com/repos/OpenSourceMalaria/OSM_To_Do_List/issues/285","labels_url":"https://api.github.com/repos/OpenSourceMalaria/OSM_To_Do_List/issues/285/labels{/name}","comments_url":"https://api.github.com/repos/OpenSourceMalaria/OSM_To_Do_List/issues/285/comments","events_url":"https://api.github.com/repos/OpenSourceMalaria/OSM_To_Do_List/issues/285/events","html_url":"https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285","id":63825059,"number":285,"title":"How do we search, store, index, annotate molecules?","user":{"login":"drc007","id":7080516,"avatar_url":"https://avatars.githubusercontent.com/u/7080516?v=3","gravatar_id":"","url":"https://api.github.com/users/drc007","html_url":"https://github.com/drc007","followers_url":"https://api.github.com/users/drc007/followers","following_url":"https://api.github.com/users/drc007/following{/other_user}","gists_url":"https://api.github.com/users/drc007/gists{/gist_id}","starred_url":"https://api.github.com/users/drc007/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drc007/subscriptions","organizations_url":"https://api.github.com/users/drc007/orgs","repos_url":"https://api.github.com/users/drc007/repos","events_url":"https://api.github.com/users/drc007/events{/privacy}","received_events_url":"https://api.github.com/users/drc007/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/OpenSourceMalaria/OSM_To_Do_List/labels/Administration","name":"Administration","color":"009800"},{"url":"https://api.github.com/repos/OpenSourceMalaria/OSM_To_Do_List/labels/High%20Priority","name":"High Priority","color":"e11d21"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":9,"created_at":"2015-03-23T20:31:53Z","updated_at":"2015-03-26T02:52:31Z","closed_at":null,"body":"I was thinking of building a file containing molecules and the associated biological data however I'm finding difficult to identify all the molecules that have been made on the project, whether there is a unique identifier for every molecule, and then find a link to any data that might have been generated on a molecule. I've seen various web pages that contain SMILES strings but I've no idea if these are comprehensive. Some have identifiers but I don't know if the identifier refers to the parent compound, if it changes with salt form or how we distinguish between batches of compound. How are OSM numbers assigned and how do check a compound has not been prepared before?\r\nAs assay data is generated how do link this to a parent/salt form/batch and how do you decide what data can be averaged?\r\nWhilst I could plough through the web pages looking for information it would soon be out of date, so it  would be better if there was a sustainable model in place for new molecules and data."},"comment":{"url":"https://api.github.com/repos/OpenSourceMalaria/OSM_To_Do_List/issues/comments/86311114","html_url":"https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-86311114","issue_url":"https://api.github.com/repos/OpenSourceMalaria/OSM_To_Do_List/issues/285","id":86311114,"user":{"login":"mattodd","id":4386101,"avatar_url":"https://avatars.githubusercontent.com/u/4386101?v=3","gravatar_id":"","url":"https://api.github.com/users/mattodd","html_url":"https://github.com/mattodd","followers_url":"https://api.github.com/users/mattodd/followers","following_url":"https://api.github.com/users/mattodd/following{/other_user}","gists_url":"https://api.github.com/users/mattodd/gists{/gist_id}","starred_url":"https://api.github.com/users/mattodd/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mattodd/subscriptions","organizations_url":"https://api.github.com/users/mattodd/orgs","repos_url":"https://api.github.com/users/mattodd/repos","events_url":"https://api.github.com/users/mattodd/events{/privacy}","received_events_url":"https://api.github.com/users/mattodd/received_events","type":"User","site_admin":false},"created_at":"2015-03-26T02:52:31Z","updated_at":"2015-03-26T02:52:31Z","body":"Yes, the use of tools to digest written information into a\nmachine-understandable form is definitely possible, but this does rely on\nthe human entering the information correctly and fully in the first place.\nI wonder how well it does with datasets, i.e. in understanding that a\ndataset contains the NMR spectrum associated with a given SMILES string,\nfor example.\nPerhaps when we've decided on a sample ELN entry to try this all out on, we\ncan see what ChemicalTagger makes of it.\n\nOne of the things that is apparently doable is to have a bot generate lab\nnotebook entries. i.e. the data etc could indeed be external and piped into\nthe ELN. I'd not considered this.\n\nOn 26 March 2015 at 12:22, miike <notifications@github.com> wrote:\n\n>  @mattodd <https://github.com/mattodd> We could feasibly do something of\n> that stuff using ChemicalTagger <http://chemicaltagger.ch.cam.ac.uk/>.\n> I've tried running it across the notebook entries with some success in the\n> past.\n>\n> As for a registration system something externally is definitely needed\n> that isn't built into Labtrove. It's possible to extract a large number of\n> OSM/MMV ids out of the current posts though.\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/285#issuecomment-86282085>\n> .\n>\n\n\n\n-- \nMATTHEW TODD | Associate Professor\nSchool of Chemistry | Faculty of Science\n\nTHE UNIVERSITY OF SYDNEY\nRm 519, F11 | The University of Sydney | NSW | 2006\nT +61 2 9351 2180  | F +61 2 9351 3329  | M +61 415 274104\nE matthew.todd@sydney.edu.au | W\nhttp://sydney.edu.au/science/chemistry/research/todd.html | W\nhttp://opensourcemalaria.org/\n\nCRICOS 00026A\nThis email plus any attachments to it are confidential. Any unauthorised\nuse is strictly prohibited. If you receive this email in error, please\ndelete it and any attachments.\n"}}