mediawikiまわり
http://en.m.wikipedia.org/wiki/DBpedia semantic-mediawiki.org/ http://www.semantic-search.info/
最後のリンクは結構面白い。
linked data / semanticweb/ rdfなマッシュアップへのsuggestion
http://lifesciencedb.g.hatena.ne.jp/nakao_mitsuteru/20091118/chap10 http://www.orally.co.jp/books/9784873114521/ https://twitter.com/32nm/status/52903495208148992
まずはidをURIで表現して、key-value をpredicateとobjectにすると、とりあえず何でもトリプルにできてマッシュアップできるはず。大抵のトリプルストアは存在していないpredicateでも動作する
thank you! @32nm
jksrc / hg18のENCODE regulation trackの設定
src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
より、かいつまんでみる。
- top levelは、superTrack (wgEncodeReg)
- 2nd levelは、container multiWig (wgEncodeRegTxn, wgEncodeRegMarkEnhH3k4me1, ...)
- 3rd levelにフツーのwig。
track wgEncodeReg superTrack on show shortLabel ENCODE Regulation longLabel ENCODE Integrated Regulation wgEncode 1 group regulation priority 1 canPack On track wgEncodeRegTxn container multiWig noInherit on type wig 0.00 2716.04 superTrack wgEncodeReg hide shortLabel Transcription longLabel ENCODE Transcription Levels Assayed by RNA-seq on 6 Cell Lines configurable on visibility full maxHeightPixels 100:30:11 showSubtrackColorOnUi on aggregate transparentOverlay transformFunc LOG viewLimits 0:4 priority 1.1 dragAndDrop subTracks track wgEncodeRegTxnGm12878 table wgEncodeCaltechRnaSeqRawSignalRep1Gm12878CellLongpolyaBb12x75 shortLabel Gm12878 longLabel Transcription of Gm12878 cells from ENCODE parent wgEncodeRegTxn type wig 0.00 2446.53 color 255,128,128 ...
jksrc / hgBbiDbLink / bigBedやbigWigファイルをloadする
src/hg/makeDb/trackDb/READMEより。
The database loading procedure is hgBbiDbLink hg19 myLocalBigWig /gbdb/hg18/bbi/myLocalBigWig.bw which is equivalent to: hgsql hg19 -e 'drop table if exists myLocalBigWig; \ create table myLocalBigWig (fileName varchar(255) not null); \ insert into myLocalBigWig values ("/gbdb/hg19/bbi/myLocalBigWig.bw");' I believe this works even if the entry is a URL to a remote bigWig file.
こちらも参考に。
http://www.mail-archive.com/genome@lists.soe.ucsc.edu/msg00924.html
jksrc / trackDB.ra / Container tracks
とかいいながら、compositeと同じようにグルーピングするスキームとして、'container'というのがある。aggregateできる、ということらしいので、最近ENCODE regulation track用に追加されたコンセプトなのかもしれない。
Container tracks are yet another way of grouping tracks together. The top level container track includes a tag of the form containerwhere currently the only container-type is "multiWig" which may only contain wig and bigWig tracks. The advantage of using "container multiWig" instead of a composite track is that container multiWig supports the "aggregate" tag that allows multiple wiggle graphs to be drawn in the same vertical space.
たとえばこんな感じ
track wgEncodeRegMarkPromoter container multiWig shortLabel Promoter H3K4Me3 longLabel ENCODE Promoter Histone Mark (H3K4Me3) on 9 Cell Lines type wig 0 30000 viewLimits 0:100 configurable on visibility full maxHeightPixels 100:30:11 aggregate transparentOverlay showSubtrackColorOnUi on windowingFunction mean priority 1.4 track wgEncodeRegMarkPromoterGm12878 shortLabel Gm12878 longLabel Promoter Histone Mark (H3K4Me3) on Gm12878 cells from ENCODE parent wgEncodeRegMarkPromoter type wig 0.00 100593.50 color 255,128,128 track wgEncodeRegMarkPromoterH1hesc shortLabel H1 ES longLabel Promoter Histone Mark (H3K4Me3) on H1 cells from ENCODE parent wgEncodeRegMarkPromoter type wig 0.00 12434.00 color 255,212,128