Scraper indexes the files listed in the TCGA's open access HTTP site as RDF.
The Schema used to represent resources in the TCGA is available as a Turtle File.
As used below, the prefix tcga represents http://purl.org/tcga/core, while tcgaRoot represents https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/.
Class and Instance diagrams of the schema are also available.
See the TCGA Data Primer and Code Tables for details on these types.
tcga:DiseaseStudytcga:CenterTypetcga:CenterDomaintcga:Platformtcga:DataTypetcga:Archivetcga:File
Data Types correspond to the directory structure:
tcgaRoot:DiseaseStudy/CenterType/CenterDomain/Platform/DataType/Archive/File
e.g.
tcgaRoot:gbm/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_GBM.MDA_RPPA_Core.Level_2.1.0.0/mdanderson.org_GBM.MDA_RPPA_Core.SuperCurve.Level_2.00da2077-778c-418a-9c92-01febd970ed8.txt
Entities of all types may have the following properties.
rdfs:labelrdf:typetcga:urltcga:lastModifiedtcga:firstSeentcga:lastSeen
Only entities of type tcga:file have the following properties.
tcga:diseaseStudytcga:centerTypetcga:centerDomaintcga:platformtcga:dataTypetcga:archive
- Install NodeJS and NPM.
- Clone this repository.
- Set the ROOT_URL and SPARQLURL environment variables.
node scraper.js.
#License Copyright (C) 2012 David E. Robbins
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.