2010-10-19

(skype with Morris)

Presentation Friday

• Talk went well
• Was expecting more feedback
• Kostavas asked on MOLGENIS

Plan BBMRI

Theme 1: fill the database

First goal: get LifeLines features included in BBMRI biobank.

• get BBMRI catalog running
• import the Excel

In the generation of the bbmri.generate : 
The bbmri_ui.xml contained  a form 

<form name="Biobanks" sortby="Name" view="list" entity="Biobank" hide_fields="Investigation,__Type,observationTargetType,individuals">

which produced error at the hide fields. I removed them , and the database was created correctly . I'm guessing something was missing and it wasn't  working. Any ideas?

In import : error for '''keys are missing: OntologyTerm.[ontology_name, term]'''

problem ...resolved!

• biobank is a kind of panel
• Lifelines is one of the biobanks
• Get from Joris is a Excel export

Next goal: import more biobank information which we get from our BBMRI-EU colleagues

Theme 2: start with 'semantic molgenis'

First goal: link MOLGENIS to external ontology

• 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

• Have Kostavas visit?
• Connect to Pedro to investigate his 'semantic molgenis' work?
• Connect to BBMRI-EU to request more data?

Virtuoso Install continues....(from yesterday)

• DONE :
  • make sure all dependencies packages are available
  • set CFLAGS, export CFLAGS, ./configure ,make install, make check (One hour & 1 GB)
  • BUT : make check FAILED . try again
    • there is a possibility of conflicting with OpenLink? installation of Virtuoso. Try Uninstall with following steps :
      • http://support.openlinksw.com/supportweb/MacFAQ#How do I uninstall OpenLink components on Mac OS X?
      1. /Applications/OpenLink Virtuoso/Virtuoso? 6.2/bin/uninstall-virtuoso.pl
         • ​http://www.mactech.com/articles/mactech/Vol.18/18.09/PerlforMacOSX/index.html
         • cd /Applications/OpenLink Virtuoso/Virtuoso? 6.2/bin * sudo perl uninstall-virtuoso.pl ...........OK !
• TODO : RUN