Changes between Version 15 and Version 16 of BBMRI


Ignore:
Timestamp:
2010-11-01T12:44:49+01:00 (14 years ago)
Author:
antonak
Comment:

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  • BBMRI

    v15 v16  
    22[[TOC()]]
    33
    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.
     4This 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). 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. 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.
    75
    86rolling plan but some endpoints
     7
    98 * Phase 1:
    109   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.
     10   1. For each biobank we have a list of features (analogous on lifelines questionaires)
     11   1. You can search for this biobanks using semantic search
     12   1. You can find related papers and people for each biobank (marco)
     13   1. You have contact information for each biobank so people can find
     14   1. Annotate all features to ontologies, first try automated using Zooma (hypothesis, will indicate suitable ontologies)
     15 * Phase 2: 1.
    1816
    19 Below the tasks to get there are described. 
     17Below the tasks to get there are described.
    2018
    2119For feedback on this project we have the following resources:
     20
    2221 * BBMRI steering committee
    2322 * Collaboration with Marco Roos (semweb interface + data on biobankers)
    2423 * All Dutch biobankers (need some power users from this group!)
    2524 * LifeLines staff as user group
     25
    2626At some point need feedback sessions.
    2727
    … …  
    3030[[bbmri_task1]]
    3131
    32 ''' Primary goal: get !LifeLines features included in BBMRI biobank as example for other biobanks. '''
     32''' Primary goal: get !LifeLines features included in BBMRI biobank as example for other biobanks. '''
     33
    3334 * get BBMRI catalog running - despoina (done)
    3435 * import the Excel - despoina (done)
    3536 * biobank is a kind of panel - despoina (done)
    36  * Get from Joris is a Excel export of LifeLines biobank metadata - joris (features, protocols)
     37 * Get from Joris is a Excel export of LifeLines biobank metadata - joris (features, protocols)
    3738 * update online version, and send email around to steering committe - morris
     39
    3840=== Task 2: Add semantic search ===
    3941[[BBMRI_task2]]
    4042
    4143''' Primary goal: to have the semantic search available for BBMRI catalog '''
     44
    4245 * reintegrate the semantic search plugin and all dependencies - despoina
    4346 * make sure that the search results make sense, i.e., list of features | biobank name - despoina
    44  * make from each element in this list a link to the right biobank (if you get stuck wait) - despoina 
     47 * make from each element in this list a link to the right biobank (if you get stuck wait) - despoina
    4548
    4649=== Task 3: Add and improve sparql interface ===
    4750''' Primary goal: make catalogue queriable by sparql '''
     51
    4852 * Add and check the sparql interface - despoina
     53   * [[bbmri_subtask3]]
    4954 * Put it in the online version - despoina
    5055 * Email Marco Roos to verify the endpoint and give feedback on it - marco
    51  * Write short wiki page on how to use [http://www.gen2phen.org/post/molgenis-and-d2r Pedro Lopes feedback] - despoina 
     56 * Write short wiki page on how to use [http://www.gen2phen.org/post/molgenis-and-d2r Pedro Lopes feedback] - despoina
    5257
    5358=== Task 4: Add biobank information from BBMR-EU catalog ===
    5459''' Primary goal: get european data into the catalog and expand model when needed '''
     60
    5561 * contact the BBMRI-EU catalog (http://gbic.target.rug.nl/trac/molgenis/wiki/BBMRI) - morris
    5662 * get data as csv or something similar - morris
    … …  
    6066=== Task 4: Explore suitable ontologies for features using Zooma ===
    6167''' Primary goal: see if we can cleanup feature descriptions by annotation with ontologies and thus improve searchability '''
     68
    6269 * put all features we have through Zooma for automated ontology assignment - despoina
    6370 * evaluate this list with an expert - rolf?
    … …  
    6774=== Task 5: Convince biobanks to use the catalogs also locally for their data ===
    6875''' Primary goal: harmonize the way that all biobanks manage their data so it is more easily integrated '''
    69 * use lifelines as example
     76
     77 * use lifelines as example
    7078
    7179== Phase 2: individual-level data harmonization and integration ==
    … …  
    7482=== Task 6: Explore use of DataSHaPeR to map between studies ===
    7583''' Primary goal: see if we an make pairwise rules between features such that data of two studies could be merged '''
     84
    7685 * need way to express mapping algorithms, can collaborate with P3G/DataSHaPER - despoina & morris
    7786 * integrate DataSHaPER rules into the catalog
    7887 * expand the catalog with some real data in collaboration with lifelines?
    7988 * test wether the rules work
     89
    8090NB this is in preparation of the BioSHARE project.
    8191
    8292=== Task 7: Exlpore use of DataSHIELD method ===
    83 ''' Primary goal: DataSHIELD allows meta analysis between projects by calculating statics locally and then sharing them between projects '''
    84 See: http://ije.oxfordjournals.org/content/early/2010/07/14/ije.dyq111
     93''' Primary goal: DataSHIELD allows meta analysis between projects by calculating statics locally and then sharing them between projects ''' See: http://ije.oxfordjournals.org/content/early/2010/07/14/ije.dyq111
    8594
    8695 * create a web service to calculate statistics locally
    8796 * have a federated interface to bridge local data into the meta analysis
    8897 * setup one of the catalogs as being the 'master' to collect and integrate the results
    89 
    90 
    91 
    92 
    93 
    9498
    9599=== Actions ===