BBMRI

Feedback group:

• BBMRI steering committee
• Collaboration with Marco Roos (semweb interface + data on biobankers)

Tasks 1: Add LifeLines metadata (features/protocols)

Primary goal: get LifeLines features included in BBMRI biobank as example for other biobanks.

• get BBMRI catalog running - despoina (done)
• import the Excel - despoina (done)
• biobank is a kind of panel - despoina (done)
• Get from Joris is a Excel export of LifeLines biobank metadata - joris (features, protocols)
• update online version, and send email around to steering committe - morris

Task 2: Add semantic search

Primary goal: to have the semantic search available for BBMRI catalog

• reintegrate the semantic search plugin and all dependencies - despoina
• make sure that the search results make sense, i.e., list of features | biobank name - despoina
• make from each element in this list a link to the right biobank (if you get stuck wait) - despoina

Task 3: Add and improve sparql interface

Primary goal: make catalogue queriable by sparql

• Add and check the sparql interface - despoina
• Put it in the online version - despoina
• Email Marco Roos to verify the endpoint and give feedback on it - marco
• Write short wiki page on how to use ​Pedro Lopes feedback - despoina

Task 4: Add biobank information from BBMR-EU catalog

Primary goal: get european data into the catalog and expand model when needed

• contact the BBMRI-EU catalog (​http://gbic.target.rug.nl/trac/molgenis/wiki/BBMRI) - morris
• get data as csv or something similar - morris
• reformat csv to match features, protocols, biobanks, contacts, and update model if something is missing - despoina
• update online version, and send email around to steering committee

Project endpoints

rolling plan but some endpoints

1. We have all Dutch biobanks in the list
2. For each biobank we have a list of features
3. You can search for this biobanks using semantic search
4. You can find related papers and people for each biobank (marco)
5. You have contact information for each biobank so people can find

• first enhance N3 file with external mapping:

• then test if we use that ontology in SPARQL query

• if works: then update the MOLGENIS model + generator

Next step: investigate ontologies that should be linked

• how about biobankers list of Marco Roos?

• disease ontology?

• material ontology?

Actions

• Connect to Pedro to investigate his 'semantic molgenis' work?

• Connect to BBMRI-EU to request more data?

(Notes)

• look into data
• cross links —> protein underlying peaks ?
• biobanks : phenotypic information e.g lifelines project data : annotate question : ARE there other data set in the world? —> merge into lifelines data …
• next step : come up with an "algorithm" that does the mapping . Let's assume we have 2 studies , we would like to merge and export the results .
• it's not really an algorithm , but more of a "correspondence " rule …If we have 2 questions - "Are they compatible "? or if not what kind of conversion should be done in order to match each other? So then we'll have a meta study ..for each biobank —> mapping
• So we have available 5 biobanks —> project on a single parameter —> bigger statistical analysis .
• How to model it ?
• RDF rules?
• parameter in one biobank / corresponding parameter in the other biobank ?
• a potential pilot would be like to

1. take 2 pheno DBs ,
2. fill with lifelines data ,
3. query that merges the set —> maybe a sparql query ?
4. different question