BBMRI

Theme 1: fill the database

First goal: get LifeLines features included in BBMRI biobank.

• get BBMRI catalog running

• import the Excel

• 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

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

• Connect to BBMRI-EU to request more data?

Log of Despoina

1. DespoinaLog/2010/02/08: Log of 2010-02-08
2. DespoinaLog/2010/02/10: Log of 2010-02-10
3. DespoinaLog/2010/02/15: Log of 2010-02-15
4. DespoinaLog/2010/02/16: Log of 2010-02-16
5. DespoinaLog/2010/02/17
6. DespoinaLog/2010/02/19: Log of 2010-02-19
7. DespoinaLog/2010/03/04: Log of 2010-03-04
8. DespoinaLog/2010/03/05: Log of 2010-03-05
9. DespoinaLog/2010/03/08: Log of 2010-03-08
10. DespoinaLog/2010/03/09: Log of 2010-03-09
11. DespoinaLog/2010/03/10: Log of 2010-03-10
12. DespoinaLog/2010/03/11: Log of 2010-03-11
13. DespoinaLog/2010/03/12: Log of 2010-03-12
14. DespoinaLog/2010/03/13
15. DespoinaLog/2010/03/14
16. DespoinaLog/2010/03/15: Log of 2010-03-15
17. DespoinaLog/2010/03/16: Log of 2010-03-16
18. DespoinaLog/2010/03/17: Log of 2010-03-17
19. DespoinaLog/2010/03/18
20. DespoinaLog/2010/03/19: Version 0.5 of term choose widget.
21. DespoinaLog/2010/03/20
22. DespoinaLog/2010/03/22
23. DespoinaLog/2010/03/23
24. DespoinaLog/2010/03/24
25. DespoinaLog/2010/03/25: Run D2R server
26. DespoinaLog/2010/03/26
27. DespoinaLog/2010/03/30
28. DespoinaLog/2010/03/31
29. DespoinaLog/2010/04/07
30. DespoinaLog/2010/04/08
31. DespoinaLog/2010/04/09
32. DespoinaLog/2010/04/12: JSON in JAVA
33. DespoinaLog/2010/04/13
34. DespoinaLog/2010/04/14: GBIC day
35. DespoinaLog/2010/04/15: Common collections error @ Peregrine in molgenis :
36. DespoinaLog/2010/04/16
37. DespoinaLog/2010/04/19
38. DespoinaLog/2010/04/20: Installation Notes
39. DespoinaLog/2010/04/21: Installation Notes .
40. DespoinaLog/2010/04/22: Mysql installation , Lucene links.
41. DespoinaLog/2010/04/23: Mysql installation with macports (macOS 10.6.3), Json libs in HVP pilot
42. DespoinaLog/2010/04/26: Add javascript libs  in molgenis  HVP pilot & Peregrine run test
43. DespoinaLog/2010/04/27: HVP pilot add functionality (build servlet in molgenis)
44. DespoinaLog/2010/04/28: HVP pilot & Lucene on Ontologies
45. DespoinaLog/2010/04/29: Next Steps , notes & links on OpenData?, nano publications & Lucene …
46. DespoinaLog/2010/05/03: Build Lucene Index (in java class)
47. DespoinaLog/2010/05/04: Problems in Molgenis update
48. DespoinaLog/2010/05/06: Create new instance of hvp_pilot after repeated errors.
49. DespoinaLog/2010/05/07: How is Lucene index build
50. DespoinaLog/2010/05/10
51. DespoinaLog/2010/05/11: SPASQL
52. DespoinaLog/2010/05/12: Why rdf and not xml
53. DespoinaLog/2010/05/17: Create Index (lucene)
54. DespoinaLog/2010/05/18
55. DespoinaLog/2010/05/19
56. DespoinaLog/2010/05/20
57. DespoinaLog/2010/05/21
58. DespoinaLog/2010/05/25: Next todos :
59. DespoinaLog/2010/05/26
60. DespoinaLog/2010/05/27
61. DespoinaLog/2010/05/28
62. DespoinaLog/2010/05/31
63. DespoinaLog/2010/06/01
64. DespoinaLog/2010/06/02
65. DespoinaLog/2010/06/03
66. DespoinaLog/2010/06/04: LUCENE Document should be created for each table (entity?) that is …
67. DespoinaLog/2010/06/07
68. DespoinaLog/2010/06/08
69. DespoinaLog/2010/06/09
70. DespoinaLog/2010/06/10
71. DespoinaLog/2010/06/11
72. DespoinaLog/2010/06/14
73. DespoinaLog/2010/06/15: debug on Lucene indexing on molgenis dbs
74. DespoinaLog/2010/06/16
75. DespoinaLog/2010/06/17: Current progress with Lucene
76. DespoinaLog/2010/06/18: Using Solrj from java
77. DespoinaLog/2010/06/20
78. DespoinaLog/2010/06/21
79. DespoinaLog/2010/06/23
80. DespoinaLog/2010/06/24
81. DespoinaLog/2010/06/25
82. DespoinaLog/2010/06/28
83. DespoinaLog/2010/06/29
84. DespoinaLog/2010/06/30
85. DespoinaLog/2010/07/01
86. DespoinaLog/2010/07/07
87. DespoinaLog/2010/09/02
88. DespoinaLog/2010/09/05: How to configure and run query expansion in molgenis4phenotype
89. DespoinaLog/2010/09/06
90. DespoinaLog/2010/09/07
91. DespoinaLog/2010/09/08
92. DespoinaLog/2010/09/09
93. DespoinaLog/2010/09/10: Install biobank_search plugin in moglenis4phenotype or animalDB and …
94. DespoinaLog/2010/09/13: biobank search plugin in molgenis4phenotype
95. DespoinaLog/2010/09/14: DONE : new configuration file in biobank search plugin
96. DespoinaLog/2010/09/15: Query expansion biobank search TODOs
97. DespoinaLog/2010/09/16: Ontocat Index created
98. DespoinaLog/2010/09/17
99. DespoinaLog/2010/09/17+: Bioassist meeting
100. DespoinaLog/2010/09/20: Biobanking hackathon II
101. DespoinaLog/2010/09/21: Alternative solution for reaching configuration file
102. DespoinaLog/2010/09/22
103. DespoinaLog/2010/09/23: Molgenis 4 phenotype :
104. DespoinaLog/2010/09/24: Molgenis4phenotype:
105. DespoinaLog/2010/09/28: Skype conference : skype call about the hackathon demo:
106. DespoinaLog/2010/09/29
107. DespoinaLog/2010/09/30: Molgenis4phenotype
108. DespoinaLog/2010/10/1: Molgenis semantics
109. DespoinaLog/2010/10/11
110. DespoinaLog/2010/10/14: virtuoso
111. DespoinaLog/2010/10/15: Bioassist meeting
112. DespoinaLog/2010/10/18: Virtuoso
113. DespoinaLog/2010/10/19: 2010-10-19
114. DespoinaLog/2010/10/20: Import data into bbmri
115. DespoinaLog/2010/10/21
116. DespoinaLog/2010/10/22
117. DespoinaLog/2010/10/25
118. DespoinaLog/2010/10/26
119. DespoinaLog/2010/10/27: Trac News item
120. DespoinaLog/2010/10/28: External Ontology
121. DespoinaLog/2010/10/29
122. DespoinaLog/2010/10/4: MolgenisSemantics?
123. DespoinaLog/2010/10/5
124. DespoinaLog/2010/10/6: Presentation for bioassit lectures.
125. DespoinaLog/2010/10/7
126. DespoinaLog/2010/10/8
127. DespoinaLog/2010/11/01
128. DespoinaLog/2010/11/04
129. DespoinaLog/2010/11/05
130. DespoinaLog/2010/11/08
131. DespoinaLog/2010/11/09: Searches on BBMRI
132. DespoinaLog/2010/11/10: Symposium on biological/bioinformatics metadata capture formats
133. DespoinaLog/2010/11/11
134. DespoinaLog/2010/11/12
135. DespoinaLog/2010/11/15
136. DespoinaLog/2010/11/16: How to install a trac plugin
137. DespoinaLog/2010/11/17
138. DespoinaLog/2010/11/22
139. DespoinaLog/2010/11/23: use case entity in pheno model
140. DespoinaLog/2010/11/24: an alternative way to upload a war file in the gbic server :
141. DespoinaLog/2010/11/25: gbic server for bbmri : & Add the auth module in BBMRI
142. DespoinaLog/2010/11/26: Trac adding captcha
143. DespoinaLog/2010/11/30
144. DespoinaLog/2010/12/01
145. DespoinaLog/2010/12/02
146. DespoinaLog/2010/12/03: How to Resolve Java Virtual Machine Out of Memory Issue
147. DespoinaLog/2010/12/06
148. DespoinaLog/2010/12/07: Biobanks missing from server
149. DespoinaLog/2010/12/08: Inconsistency with OntologyTerm table
150. DespoinaLog/2010/12/09: Inconsistency with biobank table (pheno & gcc project)
151. DespoinaLog/2010/12/10
152. DespoinaLog/2010/12/13
153. DespoinaLog/2010/12/14: Upload gcc bbmri xls data :
154. DespoinaLog/2010/12/15: import xls data (bbmri into gcc) :
155. DespoinaLog/2010/12/16
156. DespoinaLog/2010/12/20: latest version of d2rq
157. DespoinaLog/2010/12/21

Topics

• ​Lucene
• peregrine
• Text mining tools
  • ​http://www.ondex.org/
  • ​http://jtmt.sourceforge.net/
  • Online
    • ​http://www.ebi.ac.uk/webservices/whatizit/info.jsf
    • ​http://terminizer.org/
• RESTful services .
  • RESTful architecture

• SPARQL :
  • D2R server
    • D2RQ is a declarative language to describe mappings between relational database schemata and OWL/RDFS ontologies. The D2RQ Platform uses these mapping to enables applications to access a RDF-view on a non-RDF database.
    • ​How to run .
  • Resources : ​http://esw.w3.org/HCLSIG_BioRDF_Subgroup
  • Live Virtuoso Instance: ​http://lod.openlinksw.com/fct/facet.vsp