| 20 | | 1. [#AUG5 From Genetic Variants to i2b2 using NoSQL database] ''(Matteo Gabetta - Pavia)'' |
| 21 | | 1. [#AUG6 Extending i2b2 with the R Statistical Platform] |
| 22 | | 1. [#AUG7 Integrated Data Repository Toolkit (IDRT) and ETL Tools] ''(Sebastian Mate - Erlangen; Christian Bauer - Goettingen)'' |
| | 20 | 1. [#AUG5 AUG Community Projects] ''(Murphy)'' |
| | 21 | 1. [#AUG6 From Genetic Variants to i2b2 using NoSQL database] ''(Matteo Gabetta - Pavia)'' |
| | 22 | 1. [#AUG7 Identifying Normal Patients] ''(G Weber)'' |
| | 23 | 1. [#AUG8 Extending i2b2 with the R Statistical Platform] |
| | 24 | 1. [#AUG9 Integrated Data Repository Toolkit (IDRT) and ETL Tools] ''(Sebastian Mate - Erlangen; Christian Bauer - Goettingen)'' |
| | 212 | |
| | 213 | Long-term goals for i2b2: |
| | 214 | |
| | 215 | 1. Supporting Cohort Discovery |
| | 216 | 1. Supporting Big Data |
| | 217 | 1. Plugin Development: SETL - ETL Cell |
| | 218 | 1. Continued Development |
| | 219 | |
| | 220 | ==== Supporting Cohort Discovery ==== |
| | 221 | |
| | 222 | Development is underway to increase the workflow capabilities of i2b2 for clinical trials. This is called i2b2 CT. These improvements include: |
| | 223 | |
| | 224 | 1. Better visibility of patient details for users with the correct permissions. This requires the population of the patient mapping table. Patient sets can then be dragged onto a patient list tool that shows all their mapped IDs. Individual patients can then be dragged into user-defined sets that can be used in the same way as query defined patient sets. |
| | 225 | 1. Patient sets can be used to create new projects for a clinical trial, where they will have a separate project-specific ID. |
| | 226 | 1. Multi-site clinical trial projects can be set up using SHRINE. |
| | 227 | 1. Better visibility of patient details using SMART apps. |
| | 228 | 1. Individual projects may have a subset of the ontology, though can still use the same observation fact table. |
| | 229 | 1. An specific web client to be written to support the i2b2 CT workflow. |
| | 230 | |
| | 231 | ==== Supporting Big Data ==== |
| | 232 | |
| | 233 | This will be based on a flag in the Ontology Cell which will inform the CRC that it must query an external system that will return a patient set. |
| | 234 | |
| | 235 | ==== Plugin Development: SETL - ETL Cell ==== |
| | 236 | |
| | 237 | This new cell allows i2b2 to connect to web services to request specific patient level data. The new cell has two purposes. Firstly, it's main purpose appears to be to allow SMART apps to request extra data. Additionally it can be used to start a bespoke written SSIS package to load data from a file in the File Repository cell. |
| | 238 | |
| | 239 | ==== Continue Development ==== |
| | 240 | |
| | 241 | ===== Temporal Query UI Improvements ===== |
| | 242 | |
| | 243 | The definition of a temporal query has been split into two stages. |
| | 244 | |
| | 245 | 1. Define population - normal i2b2 query definition. |
| | 246 | 1. Define temporal aspects of the query. |
| | 247 | |
| | 248 | ===== PostgreSQL Support ===== |
| | 249 | |
| | 250 | Initial work to support PostgreSQL has been carried out, but further performance improvements need to be made. For this the team would like help from members of the community familiar with PostgreSQL. |
| | 251 | |
| | 252 | ===== Other Upgrades ===== |
| | 253 | |
| | 254 | 1. Support for JBoss 7.1 |
| | 255 | 1. Moved to a POJO architecture. |
| | 256 | 1. Support of SQL Server 2012. |
| | 257 | |
| | 258 | |
| 212 | | === [=#AUG5 From Genetic Variants to i2b2 using NoSQL database] === |
| 213 | | === [=#AUG6 Extending i2b2 with the R Statistical Platform] === |
| 214 | | === [=#AUG7 Integrated Data Repository Toolkit (IDRT) and ETL Tools] === |
| | 260 | |
| | 261 | ==== Suggestions for community development ==== |
| | 262 | |
| | 263 | 1. Geolocation Cell. |
| | 264 | 1. Merging of patients from different i2b2 instances probabilistically. |
| | 265 | 1. SMART App for simple NLP. |
| | 266 | |
| | 267 | ==== The Future of i2b2 ==== |
| | 268 | |
| | 269 | Funding for the i2b2 project will end in September 2014. i2b2 will still be partially funded by other projects be there will not be funding for a team to concentrate solely on i2b2. Suggested alternatives are: |
| | 270 | |
| | 271 | 1. Have commercial and community editions. |
| | 272 | 1. Increase involvement of the community in support and development. |
| | 273 | 1. Kickstarter. |
| | 274 | |
| | 275 | |
| | 276 | === [=#AUG5 AUG Community Projects] === |
| | 277 | |
| | 278 | Community projects hosted through [[https://community.i2b2.org/wiki/dashboard.action|community website]]. These include: |
| | 279 | |
| | 280 | 1. mi2b2 - for viewing images. |
| | 281 | 1. Time align - A different time line view. |
| | 282 | 1. Trends - (developed by Wake Forest) show changes of result set over time. |
| | 283 | 1. NCBO Ontology Tools. |
| | 284 | |
| | 285 | They are currently looking for people to help with the development of the web client. |
| | 286 | |
| | 287 | '''Mention was made of CRC plugins that I need to investigate.''' |
| | 288 | |
| | 289 | === [=#AUG6 From Genetic Variants to i2b2 using NoSQL database] === |
| | 290 | |
| | 291 | Various NoSQL databases available: Mongo DB, Cassandra, Apache CouchDB, Hadoop. |
| | 292 | |
| | 293 | For this project they used Apache CouchDB, which is a JSON document store. It used predefined queries written in JavaScript called a Design Document. The Design Document in compiled the first time it is run, so it is usual to run queries after deploying them to precompile all the queries. |
| | 294 | |
| | 295 | ==== Genomic Data Load Workflow ==== |
| | 296 | |
| | 297 | VCF => Annovar => CSV (Plus additional data from other systems such as patient ID) => Parser => JSON => CounchDB <-> i2b2 |
| | 298 | |
| | 299 | ==== Running Queries ==== |
| | 300 | |
| | 301 | They have created a web client plugin into which can be dragged a patient set. The plugin then count and list of the patients who have that variant. |
| | 302 | |
| | 303 | The plugin is due to be released by the end of the year. They need to do some additional testing on how well the plugin scales. |
| | 304 | |
| | 305 | |
| | 306 | === [=#AUG7 Identifying "Normal" Patients] === |
| | 307 | |
| | 308 | A presentation for the identification of normal patients for control groups. The process involved identifying criteria and that excluded the patient from being normal, such as serious illness, age range, missing details, etc. |
| | 309 | |
| | 310 | === [=#AUG8 Extending i2b2 with the R Statistical Platform] === |
| | 311 | |
| | 312 | Presentation on the use of a set of i2b2 plugins to allow R statistical platform to be used. |
| | 313 | |
| | 314 | === [=#AUG9 Integrated Data Repository Toolkit (IDRT) and ETL Tools] === |
| | 315 | |
| | 316 | ==== i2b2 Wizard ==== |
| | 317 | |
| | 318 | Presentation of the [[http://www.imi.med.uni-erlangen.de/~matesn/i2b2wizard/|i2b2 wizard]] tool that aids in the instalation of i2b2. |
| | 319 | |
| | 320 | Changes for version 2: |
| | 321 | |
| | 322 | * Different versions of i2b2 can be installed. |
| | 323 | * Works with different DBs (currently only works with oracle) |
| | 324 | |
| | 325 | ==== ETL Tools ==== |
| | 326 | |
| | 327 | Presentation of the ETL tools using the Talend ETL framework. |
