A page about the HCLS Demo given in Banff at WWW2007.
- Slides: Media:HCLS$$Banff2007Demo$Banff2007Part1.pdf, Media:HCLS$$Banff2007Demo$Banff2007Part2.pdf
- Google Maps/Allen Brain Institute/SPARQL mashup (let us know if you have trouble. Verified to work in Safari, Firefox 2 Mac/PC, IE 7/PC).
- LSW - a tool used to browse and work with ontologies.
- Browsing the data: Exhibit how to, and sample query result (best viewed using Firefox)
- Known Bugs
- Demo related SPARQL queries - describing sample queries written during development of the demo.
Please send questions, criticisms, ideas for improvements, or suggestions for additions to mailto:email@example.com
- How to install a version of the demo on a machine you control
- HCLS/DemoScript - work with June Kinoshita on developing queries against SWAN, Brainpharm, PubMed/MeSH
- HCLS/HCLSIG_DemoHomePage_HCLSIG_Demo - "home page"
- HCLS/DemoScript/Senselab_Notes - some notes on querying NeuronDB
Two servers host the RDF created to support the demonstration. One is the Neurocommons triple store, which is a project of Science Commons. DERI now also hosts a triple store containing the same material.
For the period surrounding the initial demo, machines were lent to us from HP and we are very grateful for this. Thanks to Ray Hookway for setting up the machines, and to OpenLink for Virtuoso support.
We (?) are planning release database backup files, from which the database can be reconstituted into Virtuoso, and tarballs of the RDF we loaded into the database should you want to use them in some other way.
However: Please note. This work is a prototype. We don't promise that the URIs which we use will be continued to be used in the same way, and to the extent that they resolve, be resolved in the same way. The servers will be up only until mid-June, unless we get machines donated that are able to serve beyond this trial period. Even in the case that this occurs, we plan further development on the database - After the demo period has passed graphs may change, representations may change, and your sparql queries may no longer work. We want to make progress in this work and that will mean making changes based on our and your experiences.
What's in which graph?
The triples are loaded into the triple stores in a number of separate named graphs, as described below.
- basic entrez gene information for human, mouse, rat entries, plus homologene for same species
- Transitive and other inferred relations
- Gene ontology annotations, related to entrez gene ids. (/goa4 has ebi version)
- Neurondb and Brainpharm
- 2007 MeSH to Medline associations, Medline title and dates, gene to paper (pubmed) links.
- Allen Brain Atlas gene to image section mapping (late notice - there appears to be an issue with some of this data missing - we will reload and leave a note here when done)
- http://purl.org/commons/galen/ - The full Galen ontology from the Co-ode site.
- http://purl.org/hcls/potluck - The ontologies that were on the OBO site on May 28, 2007
- http://purl.org/commons/nci/thesaurus707c/ - NCI Thesaurus, version 07.07c
- http://purl.org/hcls/radlex20071101 - Radlex owl conversion (alpha)
MeSH data are drawn from the 2007 version of MeSH, and the Medline (PubMed subset) records consulted were those from the 2007 baseline of Medline.
Shortcut to this page: http://tinyurl.com/ywalvd