{"action":"created","issue":{"url":"https://api.github.com/repos/lgatto/ProteomicsAnnotationHubData/issues/8","labels_url":"https://api.github.com/repos/lgatto/ProteomicsAnnotationHubData/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/lgatto/ProteomicsAnnotationHubData/issues/8/comments","events_url":"https://api.github.com/repos/lgatto/ProteomicsAnnotationHubData/issues/8/events","html_url":"https://github.com/lgatto/ProteomicsAnnotationHubData/issues/8","id":98049625,"number":8,"title":"MzID file","user":{"login":"lgatto","id":384198,"avatar_url":"https://avatars.githubusercontent.com/u/384198?v=3","gravatar_id":"","url":"https://api.github.com/users/lgatto","html_url":"https://github.com/lgatto","followers_url":"https://api.github.com/users/lgatto/followers","following_url":"https://api.github.com/users/lgatto/following{/other_user}","gists_url":"https://api.github.com/users/lgatto/gists{/gist_id}","starred_url":"https://api.github.com/users/lgatto/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lgatto/subscriptions","organizations_url":"https://api.github.com/users/lgatto/orgs","repos_url":"https://api.github.com/users/lgatto/repos","events_url":"https://api.github.com/users/lgatto/events{/privacy}","received_events_url":"https://api.github.com/users/lgatto/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-07-29T23:21:59Z","updated_at":"2015-07-30T21:35:19Z","closed_at":null,"body":"- lives on the AH S3 server as an `mzID` file\r\n- read directly and served directly to the user as an `mzIDfile` object\r\n```r\r\nclass: AnnotationHubMetadata\r\nAnnotationHubRoot: /var/FastRWeb/web\r\nBiocVersion: 3.2\r\nCoordinate_1_based: TRUE\r\nDataProvider: PRIDE\r\nDerivedMd5: NA\r\nDescription: Four human TMT spliked-in proteins in an Erwinia\r\n  carotovora background. Expected reporter ion ratios: Erwinia peptides:\r\n  1:1:1:1:1:1; Enolase spike (sp|P00924|ENO1_YEAST): 10:5:2.5:1:2.5:10;\r\n  BSA spike (sp|P02769|ALBU_BOVIN): 1:2.5:5:10:5:1; PhosB spike\r\n  (sp|P00489|PYGM_RABIT): 2:2:2:2:1:1; Cytochrome C spike\r\n  (sp|P62894|CYC_BOVIN): 1:1:1:1:1:2.\r\nDispatchClass: mzRident\r\nGenome: NA\r\nLocation_Prefix: http://s3.amazonaws.com/annotationhub/\r\nMaintainer: Laurent Gatto <lg390@cam.ac.uk>\r\nNotes: NA\r\nPreparerClass: PXD000001MzidToMzRidentPreparer\r\nRDataClass: mzRident\r\nRDataDateAdded: 2015-07-30\r\nRDataPath:\r\n  pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid\r\nRecipe: NA\r\nSourceLastModifiedDate: NA\r\nSourceMd5: NA\r\nSourceSize: NA\r\nSourceType: mzid\r\nSourceUrl:\r\n  http://s3.amazonaws.com/annotationhub/pride/data/archive/2012/03/PXD000001/\r\nSourceVersion: 2015-07-29 23:58:20\r\nSpecies: Erwinia carotovora\r\nTags: Proteomics TMT6 LTQ Orbitrap Velos PMID:23692960\r\nTaxonomyId: 554\r\nTitle: PXD000001: MS-GF+ identiciation data\r\n```\r\n\r\nI think that the `SourceUrl` is missing the filename because it is not yet on the server, or just not accessible."},"comment":{"url":"https://api.github.com/repos/lgatto/ProteomicsAnnotationHubData/issues/comments/126497685","html_url":"https://github.com/lgatto/ProteomicsAnnotationHubData/issues/8#issuecomment-126497685","issue_url":"https://api.github.com/repos/lgatto/ProteomicsAnnotationHubData/issues/8","id":126497685,"user":{"login":"sonali-bioc","id":6373953,"avatar_url":"https://avatars.githubusercontent.com/u/6373953?v=3","gravatar_id":"","url":"https://api.github.com/users/sonali-bioc","html_url":"https://github.com/sonali-bioc","followers_url":"https://api.github.com/users/sonali-bioc/followers","following_url":"https://api.github.com/users/sonali-bioc/following{/other_user}","gists_url":"https://api.github.com/users/sonali-bioc/gists{/gist_id}","starred_url":"https://api.github.com/users/sonali-bioc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sonali-bioc/subscriptions","organizations_url":"https://api.github.com/users/sonali-bioc/orgs","repos_url":"https://api.github.com/users/sonali-bioc/repos","events_url":"https://api.github.com/users/sonali-bioc/events{/privacy}","received_events_url":"https://api.github.com/users/sonali-bioc/received_events","type":"User","site_admin":false},"created_at":"2015-07-30T21:35:19Z","updated_at":"2015-07-30T21:35:19Z","body":"This recipe looks good too !\r\n\r\n```{r}\r\n> tail(ah)\r\nAnnotationHub with 6 records\r\n# snapshotDate(): 2015-07-30\r\n# $dataprovider: PRIDE, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/\r\n# $species: Erwinia carotovora, Lactobacillus jensenii_JV-V16, Methanocaldoc...\r\n# $rdataclass: OrgDb, AAStringSet, MSnSet, mzRident, mzRpwiz\r\n# additional mcols(): taxonomyid, genome, description, tags, sourceurl,\r\n#   sourcetype\r\n# retrieve records with, e.g., 'object[[\"AH49004\"]]'\r\n\r\n            title\r\n  AH49004 | org.Methanocaldococcus_infernus_ME.eg.sqlite\r\n  AH49005 | org.Lactobacillus_jensenii_JV-V16.eg.sqlite\r\n  AH49006 | PXD000001: Erwinia carotovora and spiked-in protein fasta file\r\n  AH49007 | PXD000001: Peptide-level quantitation data\r\n  AH49008 | PXD000001: raw mass spectrometry data\r\n  AH49009 | PXD000001: MS-GF+ identiciation data\r\n> mzid <- ah[['AH49009']]\r\nretrieving 1 resource\r\n  |======================================================================| 100%\r\nThere were 50 or more warnings (use warnings() to see the first 50)\r\n> class(mzid)\r\n[1] \"mzRident\"\r\nattr(,\"package\")\r\n[1] \"mzR\"\r\n> mzid\r\nIdentification file handle.\r\nFilename:  55315\r\nNumber of psms:  5759\r\n\r\n```"}}