http://colil.dbcls.jp:18052/sparql?query=define%20sql%3Adescribe-mode%20%22CBD%22%20%20DESCRIBE%20%3Chttp%3A%2F%2Fpurl.jp%2Fbio%2F10%2Fcolil%2Fid%2F19906727%3E&output=application%2Fatom%2Bxml2024-03-28T20:28:06.703274ZOData Service and Descriptor DocumentnodeID://b4182790692024-03-28T20:28:06.703274Z2nodeID://b4182786852024-03-28T20:28:06.703274Z8nodeID://b4182791692024-03-28T20:28:06.703274Z2nodeID://b4182787852024-03-28T20:28:06.703274Z3nodeID://b4182788852024-03-28T20:28:06.703274Z2nodeID://b4182786822024-03-28T20:28:06.703274Z9nodeID://b4182790662024-03-28T20:28:06.703274Z2nodeID://b4182791662024-03-28T20:28:06.703274Z2nodeID://b4182789852024-03-28T20:28:06.703274Z2nodeID://b4182787822024-03-28T20:28:06.703274Z3nodeID://b4182788822024-03-28T20:28:06.703274Z2nodeID://b4182789822024-03-28T20:28:06.703274Z2nodeID://b4182786902024-03-28T20:28:06.703274Z7nodeID://b4182787902024-03-28T20:28:06.703274Z3nodeID://b4182790712024-03-28T20:28:06.703274Z2nodeID://b4182788902024-03-28T20:28:06.703274Z2nodeID://b4182791712024-03-28T20:28:06.703274Z2nodeID://b4182789902024-03-28T20:28:06.703274Z2nodeID://b4182787362024-03-28T20:28:06.703274Z4nodeID://b4182788362024-03-28T20:28:06.703274Z2nodeID://b4182790172024-03-28T20:28:06.703274Z2nodeID://b4182791172024-03-28T20:28:06.703274Z2nodeID://b4182789362024-03-28T20:28:06.703274Z2nodeID://b4182787332024-03-28T20:28:06.703274Z4nodeID://b4182788332024-03-28T20:28:06.703274Z3nodeID://b4182790142024-03-28T20:28:06.703274Z2nodeID://b4182791142024-03-28T20:28:06.703274Z2nodeID://b4182789332024-03-28T20:28:06.703274Z2nodeID://b4182786672024-03-28T20:28:06.703274Z13nodeID://b4182787672024-03-28T20:28:06.703274Z3nodeID://b4182788672024-03-28T20:28:06.703274Z2nodeID://b4182789672024-03-28T20:28:06.703274Z2nodeID://b4182791482024-03-28T20:28:06.703274Z2nodeID://b4182790562024-03-28T20:28:06.703274Z2nodeID://b4182786722024-03-28T20:28:06.703274Z12nodeID://b4182787722024-03-28T20:28:06.703274Z3nodeID://b4182791562024-03-28T20:28:06.703274Z2nodeID://b4182788722024-03-28T20:28:06.703274Z2nodeID://b4182790532024-03-28T20:28:06.703274Z2nodeID://b4182791532024-03-28T20:28:06.703274Z2nodeID://b4182789722024-03-28T20:28:06.703274Z2nodeID://b4182790872024-03-28T20:28:06.703274Z2nodeID://b4182787182024-03-28T20:28:06.703274Z5nodeID://b4182788182024-03-28T20:28:06.703274Z3nodeID://b4182789182024-03-28T20:28:06.703274Z2nodeID://b4182790922024-03-28T20:28:06.703274Z2nodeID://b4182787232024-03-28T20:28:06.703274Z5nodeID://b4182788232024-03-28T20:28:06.703274Z3nodeID://b4182790042024-03-28T20:28:06.703274Z2nodeID://b4182791042024-03-28T20:28:06.703274Z2nodeID://b4182789232024-03-28T20:28:06.703274Z2nodeID://b4182787202024-03-28T20:28:06.703274Z5nodeID://b4182788202024-03-28T20:28:06.703274Z3nodeID://b4182790012024-03-28T20:28:06.703274Z2nodeID://b4182791012024-03-28T20:28:06.703274Z2nodeID://b4182789202024-03-28T20:28:06.703274Z2nodeID://b4182787572024-03-28T20:28:06.703274Z4nodeID://b4182788572024-03-28T20:28:06.703274Z2nodeID://b4182790382024-03-28T20:28:06.703274Z2nodeID://b4182787542024-03-28T20:28:06.703274Z4nodeID://b4182789572024-03-28T20:28:06.703274Z2nodeID://b4182791382024-03-28T20:28:06.703274Z2nodeID://b4182788542024-03-28T20:28:06.703274Z2nodeID://b4182790352024-03-28T20:28:06.703274Z2nodeID://b4182789542024-03-28T20:28:06.703274Z2nodeID://b4182791352024-03-28T20:28:06.703274Z2nodeID://b4182786882024-03-28T20:28:06.703274Z8nodeID://b4182787882024-03-28T20:28:06.703274Z3nodeID://b4182788882024-03-28T20:28:06.703274Z2nodeID://b4182789882024-03-28T20:28:06.703274Z2nodeID://b4182790432024-03-28T20:28:06.703274Z2nodeID://b4182791432024-03-28T20:28:06.703274Z2nodeID://b4182790402024-03-28T20:28:06.703274Z2nodeID://b4182791402024-03-28T20:28:06.703274Z2nodeID://b4182786962024-03-28T20:28:06.703274Z7nodeID://b4182787962024-03-28T20:28:06.703274Z3nodeID://b4182788962024-03-28T20:28:06.703274Z2nodeID://b4182786932024-03-28T20:28:06.703274Z7nodeID://b4182790772024-03-28T20:28:06.703274Z2nodeID://b4182791772024-03-28T20:28:06.703274Z2nodeID://b4182789962024-03-28T20:28:06.703274Z2nodeID://b4182787932024-03-28T20:28:06.703274Z3nodeID://b4182790742024-03-28T20:28:06.703274Z2nodeID://b4182788932024-03-28T20:28:06.703274Z2nodeID://b4182791742024-03-28T20:28:06.703274Z2nodeID://b4182789932024-03-28T20:28:06.703274Z2nodeID://b4182787082024-03-28T20:28:06.703274Z5nodeID://b4182788082024-03-28T20:28:06.703274Z3nodeID://b4182787052024-03-28T20:28:06.703274Z6nodeID://b4182789082024-03-28T20:28:06.703274Z2nodeID://b63875602024-03-28T20:28:06.703274Zorg) via DAS [distributed annotation system, (>>5<<)]. Once COSMIC DAS tracks are turned on (either via Ensembl configuration or a link on the gene or mutation summary pages), COSMIC annotations for both genes and mutations can be examined in a genomic context (Figure 3).nodeID://b4182788052024-03-28T20:28:06.703274Z3nodeID://b63875612024-03-28T20:28:06.703274ZA much lengthier discussion of the data in COSMIC and its navigation is available as a Protocol document (>>6<<). Figure 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these large-scale studies in COSMIC, the curation systems have now been extended and the inclusion of such data has begun with the release of the Sjoblom et al. screen of breast and colorectal tumours in the full CCDS gene set (>>8<<). While the curation of point mutations in COSMIC is an ongoing activity, the number of uncurated genes remaining is rapidly reducing and has allowed a redirection of effort to include oncogenic gene fusion events, with many more genesnodeID://b4182788552024-03-28T20:28:06.703274Z2nodeID://b4182789552024-03-28T20:28:06.703274Z2nodeID://b63875482024-03-28T20:28:06.703274Zmutations in COSMIC is an ongoing activity, the number of uncurated genes remaining is rapidly reducing and has allowed a redirection of effort to include oncogenic gene fusion events, with many more genes involved than point mutations (>>1<<). The genetic analysis of human cancer has also begun to lose its coding-domain focus, with full-genome resequencing of tumours now underway, generating tens of thousands of mutations per sample, together with many genomic rearrangements.nodeID://b63875492024-03-28T20:28:06.703274ZThese are now being released into COSMIC, using the Circos diagram (>>4<<) as a basis for summarizing genome-wide data, particularly useful for presenting complex intra- and inter-chromsosmal 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contentnodeID://b4182791552024-03-28T20:28:06.703274Z2nodeID://b4182789742024-03-28T20:28:06.703274Z2nodeID://b63875512024-03-28T20:28:06.703274ZGenes are highlighted for curation by their presence in the Cancer Gene Census [(>>1<<); http://www.sanger.ac.uk/genetics/CGP/Census/], focusing on these well-characterized genes and collecting large quantities of information (for example, over 13 000 instances of 105 unique sequence variants have been curated in KRAS).nodeID://b63875522024-03-28T20:28:06.703274ZCancer-promoting gene fusion mutations are also being curated, as there are many more genes promoting tumour growth via fusion events than point mutations (>>1<<). The literature curation process is largely manual, gradually accumulating the quantity of data currently available over 9 years. As information is entered to COSMIC by dedicated trained curators, software systems check each datapointnodeID://b63875532024-03-28T20:28:06.703274ZMore recently, CGP data includes low coverage whole genome resequencing screens (>>2<<), utilizing next-generation sequencing technologies which can precisely identify genome-level rearrangements previously invisible in both karyotypic and candidate gene screen procedures.nodeID://b63875542024-03-28T20:28:06.703274ZThis mutation ‘syntax’ is derived from the HGVS nomenclature recommendations (>>3<<). Coding domain annotations receive a ‘c.’ syntax, indicating the mutation is located on a cDNA CDS co-ordinate and a ‘p.’ syntax indicating an amino acid co-ordinate. Gene fusions receive an ‘r.’ syntax indicating the co-ordinate isnodeID://b63875552024-03-28T20:28:06.703274Zfuture worknodeID://b63875562024-03-28T20:28:06.703274ZEspecially designed for the mining of complex datasets, Biomart (>>7<<) allows the specification of any number of predicate sets, querying the COSMIC database and returning the appropriate data in tabulated form, with links back in to the COSMIC websystem where appropriate.nodeID://b63875572024-03-28T20:28:06.703274Zdata accessnodeID://b63875582024-03-28T20:28:06.703274ZSamples which have undergone whole-genome sequencing receive summary annotation in the form of a ‘circos’ diagram [Figure 2; (>>4<<)]. This is due to the quantity and complexity of the data collected by these studies, which includes extensive lists of coding and non-coding point mutations, copy number variations and genomic rearrangements.nodeID://b4182790632024-03-28T20:28:06.703274Z2nodeID://b4182791632024-03-28T20:28:06.703274Z2nodeID://b63875592024-03-28T20:28:06.703274ZCOSMIC has now standardized on Circos diagrams (>>4<<) to display genome-wide mutation analyses for a sample. Concentric rings display different data for the same sample, all located to the same genomic co-ordinates.nodeID://b4182790602024-03-28T20:28:06.703274Z2nodeID://b4182791602024-03-28T20:28:06.703274Z2nodeID://b4182790972024-03-28T20:28:06.703274Z2nodeID://b4182790942024-03-28T20:28:06.703274Z2nodeID://b4182787282024-03-28T20:28:06.703274Z5nodeID://b4182788282024-03-28T20:28:06.703274Z3nodeID://b4182790092024-03-28T20:28:06.703274Z2nodeID://b4182791092024-03-28T20:28:06.703274Z2nodeID://b4182789282024-03-28T20:28:06.703274Z2nodeID://b4182787252024-03-28T20:28:06.703274Z5nodeID://b4182788252024-03-28T20:28:06.703274Z3nodeID://b4182790062024-03-28T20:28:06.703274Z2nodeID://b4182791062024-03-28T20:28:06.703274Z2nodeID://b4182789252024-03-28T20:28:06.703274Z2nodeID://b4182787222024-03-28T20:28:06.703274Z5nodeID://b4182788222024-03-28T20:28:06.703274Z3nodeID://b4182789222024-03-28T20:28:06.703274Z2nodeID://b4182787592024-03-28T20:28:06.703274Z4nodeID://b4182788592024-03-28T20:28:06.703274Z2nodeID://b4182789592024-03-28T20:28:06.703274Z2nodeID://b4182787302024-03-28T20:28:06.703274Z4nodeID://b4182788302024-03-28T20:28:06.703274Z3nodeID://b4182790112024-03-28T20:28:06.703274Z2nodeID://b4182791112024-03-28T20:28:06.703274Z2nodeID://b4182789302024-03-28T20:28:06.703274Z2nodeID://b4182786642024-03-28T20:28:06.703274Z21nodeID://b4182790482024-03-28T20:28:06.703274Z2nodeID://b4182787642024-03-28T20:28:06.703274Z3nodeID://b4182790452024-03-28T20:28:06.703274Z2nodeID://b4182788642024-03-28T20:28:06.703274Z2nodeID://b4182787612024-03-28T20:28:06.703274Z4nodeID://b4182789642024-03-28T20:28:06.703274Z2nodeID://b4182791452024-03-28T20:28:06.703274Z2nodeID://b4182788612024-03-28T20:28:06.703274Z2nodeID://b4182790422024-03-28T20:28:06.703274Z2nodeID://b4182791422024-03-28T20:28:06.703274Z2nodeID://b4182789612024-03-28T20:28:06.703274Z2nodeID://b4182786982024-03-28T20:28:06.703274Z6nodeID://b4182787982024-03-28T20:28:06.703274Z3nodeID://b4182786952024-03-28T20:28:06.703274Z7nodeID://b4182788982024-03-28T20:28:06.703274Z2nodeID://b4182790792024-03-28T20:28:06.703274Z2nodeID://b4182791792024-03-28T20:28:06.703274Z2nodeID://b4182789982024-03-28T20:28:06.703274Z2nodeID://b4182787952024-03-28T20:28:06.703274Z3nodeID://b4182788952024-03-28T20:28:06.703274Z2nodeID://b4182789952024-03-28T20:28:06.703274Z2nodeID://b4182790502024-03-28T20:28:06.703274Z2nodeID://b4182791502024-03-28T20:28:06.703274Z2nodeID://b4182787072024-03-28T20:28:06.703274Z5nodeID://b4182788072024-03-28T20:28:06.703274Z3nodeID://b4182790842024-03-28T20:28:06.703274Z2nodeID://b4182789072024-03-28T20:28:06.703274Z2nodeID://b4182790812024-03-28T20:28:06.703274Z2nodeID://b4182787152024-03-28T20:28:06.703274Z5nodeID://b4182788152024-03-28T20:28:06.703274Z3nodeID://b4182787122024-03-28T20:28:06.703274Z5nodeID://b4182789152024-03-28T20:28:06.703274Z2nodeID://b4182788122024-03-28T20:28:06.703274Z3nodeID://b4182789122024-03-28T20:28:06.703274Z2nodeID://b4182787492024-03-28T20:28:06.703274Z4nodeID://b4182788492024-03-28T20:28:06.703274Z2nodeID://b4182787462024-03-28T20:28:06.703274Z4nodeID://b4182789492024-03-28T20:28:06.703274Z2nodeID://b4182788462024-03-28T20:28:06.703274Z2nodeID://b4182790272024-03-28T20:28:06.703274Z2nodeID://b4182791272024-03-28T20:28:06.703274Z2nodeID://b4182789462024-03-28T20:28:06.703274Z2http://purl.jp/bio/10/colil/id/199067272024-03-28T20:28:06.703274ZPMC010.1093%2Fnar%2Fgkp995nodeID://b4182787512024-03-28T20:28:06.703274Z4nodeID://b4182788512024-03-28T20:28:06.703274Z2nodeID://b4182790322024-03-28T20:28:06.703274Z2nodeID://b4182791322024-03-28T20:28:06.703274Z2nodeID://b4182789512024-03-28T20:28:06.703274Z2