Changes between Version 7 and Version 8 of BBMRI
- Timestamp:
- 2010-11-01T10:09:35+01:00 (14 years ago)
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BBMRI
v7 v8 1 = BBMRI =1 = BBMRI catalogues project = 2 2 [[TOC()]] 3 3 4 This project aims to produce biobanks catalogs that can be used centrally (e.g. by BBMRI-NL headquarters) and locally (e.g. by local biobanks that need a database to manage their studies). 5 In the first phase we will only deal with metadata and not individual level data. That means we only have biobanks, cohorts, protocols and features but not individuals. 6 In the second phase we will add software features for individual level data, for example for meta analysis and data harmonization. This project is related to NBIC biobanks, LifeLines, GEN2PHEN, and EU-BioSHARE. 7 8 rolling plan but some endpoints 9 * Phase 1: 10 1. We have all Dutch biobanks in the list 11 2. For each biobank we have a list of features (analogous on lifelines questionaires) 12 3. You can search for this biobanks using semantic search 13 4. You can find related papers and people for each biobank (marco) 14 5. You have contact information for each biobank so people can find 15 6. Annotate all features to ontologies, first try automated using Zooma (hypothesis, will indicate suitable ontologies) 16 * Phase 2: 17 1. 18 19 Below the tasks to get there are described. 20 4 21 == Feedback group: == 22 For feedback on this project we have the following resoruces: 5 23 * BBMRI steering committee 6 24 * Collaboration with Marco Roos (semweb interface + data on biobankers) 7 25 * All Dutch biobankers (need some power users from this group!) 8 * Maybe first start withLifeLines staff as user group26 * LifeLines staff as user group 9 27 At some point need feedback sessions. 10 28 11 == Tasks 1: Add !LifeLines metadata (features/protocols) == 12 ==== Primary goal: get !LifeLines features included in BBMRI biobank as example for other biobanks. ==== 29 == Phase 1: biobank metadata catalog == 30 31 === Tasks 1: Add !LifeLines metadata (features/protocols) === 32 ''' Primary goal: get !LifeLines features included in BBMRI biobank as example for other biobanks. ''' 13 33 * get BBMRI catalog running - despoina (done) 14 34 * import the Excel - despoina (done) … … 17 37 * update online version, and send email around to steering committe - morris 18 38 19 == Task 2: Add semantic search==20 ==== Primary goal: to have the semantic search available for BBMRI catalog ==== 39 === Task 2: Add semantic search === 40 ''' Primary goal: to have the semantic search available for BBMRI catalog ''' 21 41 * reintegrate the semantic search plugin and all dependencies - despoina 22 42 * make sure that the search results make sense, i.e., list of features | biobank name - despoina 23 43 * make from each element in this list a link to the right biobank (if you get stuck wait) - despoina 24 44 25 == Task 3: Add and improve sparql interface26 ==== Primary goal: make catalogue queriable by sparql ==== 45 === Task 3: Add and improve sparql interface === 46 ''' Primary goal: make catalogue queriable by sparql ''' 27 47 * Add and check the sparql interface - despoina 28 48 * Put it in the online version - despoina … … 30 50 * Write short wiki page on how to use [http://www.gen2phen.org/post/molgenis-and-d2r Pedro Lopes feedback] - despoina 31 51 32 == Task 4: Add biobank information from BBMR-EU catalog==33 ==== Primary goal: get european data into the catalog and expand model when needed ==== 52 === Task 4: Add biobank information from BBMR-EU catalog === 53 ''' Primary goal: get european data into the catalog and expand model when needed ''' 34 54 * contact the BBMRI-EU catalog (http://gbic.target.rug.nl/trac/molgenis/wiki/BBMRI) - morris 35 55 * get data as csv or something similar - morris … … 37 57 * update online version, and send email around to steering committee 38 58 39 == Task 4: Explore suitable ontologies for features using Zooma==40 ==== Primary goal: see if we can cleanup feature descriptions by annotation with ontologies and thus improve searchability ==== 59 === Task 4: Explore suitable ontologies for features using Zooma === 60 ''' Primary goal: see if we can cleanup feature descriptions by annotation with ontologies and thus improve searchability ''' 41 61 * put all features we have through Zooma for automated ontology assignment - despoina 42 62 * evaluate this list with an expert - rolf? … … 44 64 * do an experiment with users to see if this improves searchability - despoina 45 65 46 == Task 5: Convince biobanks to use the catalogs also locally for their data==47 ==== Primary goal: harmonize the way that all biobanks manage their data so it is more easily integrated ==== 66 === Task 5: Convince biobanks to use the catalogs also locally for their data === 67 ''' Primary goal: harmonize the way that all biobanks manage their data so it is more easily integrated ''' 48 68 * use lifelines as example 49 69 70 == Phase 2: individual-level data harmonization and integration == 50 71 Beyond original remit (so not only metadata but also data!) 51 72 52 == Task 6: Explore use of DataSHaPeR to map between studies==53 ==== Primary goal: see if we an make pairwise rules between features such that data of two studies could be merged ==== 73 === Task 6: Explore use of DataSHaPeR to map between studies === 74 ''' Primary goal: see if we an make pairwise rules between features such that data of two studies could be merged ''' 54 75 * need way to express mapping algorithms, can collaborate with P3G/DataSHaPER - despoina & morris 55 76 * integrate DataSHaPER rules into the catalog … … 58 79 NB this is in preparation of the BioSHARE project. 59 80 60 == Task 7: Exlpore use of DataSHIELD method==61 ==== Primary goal: DataSHIELD allows meta analysis between projects by calculating statics locally and then sharing them between projects ==== 81 === Task 7: Exlpore use of DataSHIELD method === 82 ''' Primary goal: DataSHIELD allows meta analysis between projects by calculating statics locally and then sharing them between projects ''' 62 83 See: http://ije.oxfordjournals.org/content/early/2010/07/14/ije.dyq111 63 84 … … 66 87 * setup one of the catalogs as being the 'master' to collect and integrate the results 67 88 68 == Project endpoints ==69 rolling plan but some endpoints70 1. We have all Dutch biobanks in the list71 2. For each biobank we have a list of features (analogous on lifelines questionaires)72 3. You can search for this biobanks using semantic search73 4. You can find related papers and people for each biobank (marco)74 5. You have contact information for each biobank so people can find75 6. Optional? Annotate all features to ontologies, first try automated using Zooma (hypothesis, will indicate suitable ontologies)76 7.77 89 78 ==== Next step: investigate ontologies that should be linked ====79 * how about biobankers list of Marco Roos?80 90 81 * disease ontology?82 91 83 * material ontology? 92 84 93 85 94 === Actions === … … 96 105 * So we have available 5 biobanks —> project on a single parameter —> bigger statistical analysis . 97 106 * How to model it ? 98 * RDF rules? 107 * RDF rules?å 99 108 * parameter in one biobank / corresponding parameter in the other biobank ? 100 109 * a potential pilot would be like to
