wiki:DespoinaLog/2010/10/19

Version 8 (modified by antonak, 14 years ago) (diff)

--

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]'''
  • 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)
  • TODO : RUN