{"action":"created","issue":{"url":"https://api.github.com/repos/dhimmel/lincs/issues/2","labels_url":"https://api.github.com/repos/dhimmel/lincs/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/dhimmel/lincs/issues/2/comments","events_url":"https://api.github.com/repos/dhimmel/lincs/issues/2/events","html_url":"https://github.com/dhimmel/lincs/issues/2","id":118673033,"number":2,"title":"Code to generate l1000.db or the downloadable l1000.db","user":{"login":"zhilongjia","id":1230436,"avatar_url":"https://avatars.githubusercontent.com/u/1230436?v=3","gravatar_id":"","url":"https://api.github.com/users/zhilongjia","html_url":"https://github.com/zhilongjia","followers_url":"https://api.github.com/users/zhilongjia/followers","following_url":"https://api.github.com/users/zhilongjia/following{/other_user}","gists_url":"https://api.github.com/users/zhilongjia/gists{/gist_id}","starred_url":"https://api.github.com/users/zhilongjia/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zhilongjia/subscriptions","organizations_url":"https://api.github.com/users/zhilongjia/orgs","repos_url":"https://api.github.com/users/zhilongjia/repos","events_url":"https://api.github.com/users/zhilongjia/events{/privacy}","received_events_url":"https://api.github.com/users/zhilongjia/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-11-24T18:23:42Z","updated_at":"2015-11-24T18:50:09Z","closed_at":null,"body":"As shown in database.ipynb, there is a large-size l1000.db file, containing the gene expression profiles and meta data of lincs. Here could you publish the code to produce the l1000.db and/or the l1000.db itself? Thank you."},"comment":{"url":"https://api.github.com/repos/dhimmel/lincs/issues/comments/159370020","html_url":"https://github.com/dhimmel/lincs/issues/2#issuecomment-159370020","issue_url":"https://api.github.com/repos/dhimmel/lincs/issues/2","id":159370020,"user":{"login":"dhimmel","id":1117703,"avatar_url":"https://avatars.githubusercontent.com/u/1117703?v=3","gravatar_id":"","url":"https://api.github.com/users/dhimmel","html_url":"https://github.com/dhimmel","followers_url":"https://api.github.com/users/dhimmel/followers","following_url":"https://api.github.com/users/dhimmel/following{/other_user}","gists_url":"https://api.github.com/users/dhimmel/gists{/gist_id}","starred_url":"https://api.github.com/users/dhimmel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dhimmel/subscriptions","organizations_url":"https://api.github.com/users/dhimmel/orgs","repos_url":"https://api.github.com/users/dhimmel/repos","events_url":"https://api.github.com/users/dhimmel/events{/privacy}","received_events_url":"https://api.github.com/users/dhimmel/received_events","type":"User","site_admin":false},"created_at":"2015-11-24T18:50:08Z","updated_at":"2015-11-24T18:50:08Z","body":"This reply is in the context of the repository at commit 093dc3a0497028ad2b9549a3f9fa12f8ce38461f.\r\n\r\n## Database contents\r\n\r\n`l1000.db` contains the following tables:\r\n\r\n+ `cells`: observations are cell types\r\n+ `perts`: observations are pertrubagens\r\n+ `sigs`: observations are signatures\r\n+ `similarities`: observations are perturbagen pairs\r\n+ `unichem`: observations are perturbagen to external identifier mappings\r\n\r\n`similarities` and `unichem` only have information for small molecule compounds with InChI strings.\r\n\r\nCurrently, the database does not contain any gene information (such as differential expression). If you want our consensus expression signatures, [look here](http://doi.org/10.15363/thinklab.d43#6).\r\n\r\n## Downloading `l1000.db`\r\n\r\nI didn't originally upload the database because of it's size (18.4 GB). If anyone knows of a free repository for large files, let us know. I've posted the database file for download (http://dipper.ucsf.edu/l1000.db). This location is only temporary, so don't rely on its permanence.\r\n\r\n## Recreating `l1000.db`\r\n\r\nIf you clone the repository, you should be able the recreate the database by running the following notebooks in order (written for Python 3.4):\r\n\r\n1. `database.ipynb`\r\n2. `unichem.ipynb`\r\n3. `chemical-similarity.ipynb`"}}