Changes between Initial Version and Version 1 of DespoinaLog/2010/11/10

Timestamp:

2010-11-11T10:43:05+01:00 (14 years ago)

Author:

antonak

Comment:

--

DespoinaLog/2010/11/10

@@ +1 @@
+= Symposium on biological/bioinformatics metadata capture formats =
+10 /11/2010 
+
+study capture symposium 
+
+(open software )
+
+i3cube (not biological point of view
+
+open bis
+
+labkey
+
+isa creator
+
+wikilims
+
+galaxy
+
+bioeclipse
+
+============================================
+
+sysmo db :
+
+sysmo.net
+
+system biology 
+
+accèss permissions! groups of (whitelist /black list)
+
+MIAME , MIAPE , isainfrustructure (tabular)
+
+els………….---> rightfield(free to download)  :tooling for annotation inside els => drop down micraaray analysis template retrieve ontology terms….---> back to excels --> 
+
+csvmagetab-->rdf (convert magetab/csv to rdf )(SIMIRAL WORK)
+
+sbml
+
+jerm
+
+sysmo-db.org
+
+========================================
+
+molgenis
+
+inconsistencies in model--> annotate in ontology (additional validation??) 
+
+==============================
+
+FDA director :
+
+2 genotypes --> 2 diets 
+
+environment,vars
+
+….
+
+model : core model that can be admined by a user from wizards (ui)
+
+xls exporter
+
+development (reload css js or both in the ui )
+
+=========================================
+
+sequencing
+
+(report, statistics-maps-rwa data, output, )
+
+mappability  -->  quality measurement 
+
+there is a lims so basically the problem of storing and presenting the data and the analysis is a matter of admininstratation
+
+=============================
+
+proteomics
+
+samples--> depletion--> digestion --> analysis (sneaps, biomarker candidates)
+
+(preparation protocols, )
+
+mass spectrometer, raw data, sanders format and then processing(quantitative, peptide/protein identification 
+
+labeling, statistical analysis , '''knowledge discovery pathway identification''' (NN , name entity recognition algorithms >machine learning?)) (still a new , difficult task, a lot of things to be done)
+
+the same problems apply in metabolomics. ( )
+
+wrap2d : nbbpp.nl/warp2d.html
+
+================discussion 
+
+rdf
+
+there are some components that can be exchanged . 
+
+plone  in python dbnp
+
+ruby on rails --> jrybu 
+
+===== 
+
+morris on data models : 
+
+experiences form various projects 
+
+like gen2phen 
+
+many models
+
+magetab,(idf, sdrf, )
+
+xgap, 
+
+pheno fuge magetab++
+
+isatabm chado, hl7 
+
+=======================
+
+linked data approach 
+
+computational experiment (modeling ) in rdf ?
+
+biordf  , 
+
+swobjects 
+
+create a spqrql endpoint 
+
+query rewrinting to sql and sparql 
+
+sourceforge……./apps/mediawiki/swobjects
+
+;
+
+mores attic object --> CHAINING buffered : if then else rules …..
+
+do you have an example that actually connects these different datasest in 15 ????
+
+h eirwnia ienia to to minebiotext douleuei mono me gene idss den mporeis na ta vreis .
+
+SADI -fy the components (AIDA 
+
+===================================
+
+Scientific discourse (harvard) data & experiment 
+
+swan,sioc: ontology fro social networking  
+
+OBi, Mo efo 
+
+!MyExperiment,
+
+AO (annotation)
+
+Build an application ontology to integrate  
+
+
+= Next steps  =
+(spqrql endpoint in the server (gbic) include d2rq application 
+
+after a talk with christie : try to connect with concept wiki . maybe each term in the 
+
+database (ontologyerm???0 with the corresponding  term  in concept wiki . 
+
+also we'll talk about this in the conference "connecting biobanks"      
+
+//todo : add a connection to concept wiki for each term. (this will be a next step in the bbmri wiki)
+
+=======================================
+
+10/11/2010
+
+Search results : 
+
+searching the name 
+
+search for
+
+acronym is working 
+
+description is working 
+
+so for lastName not working : is it included in configuration file? twice 
+
+remove one and then try lastname instead of !LastName
+
+So the last name is included in the index. : but cannot be found as 
+
+All : 1st (contacts_lastName)as !InsertFieldValue inserted in Indexstored,indexed,tokenized<contacts_lastName:[de Leeuw, Kroon]>
+
+TODO : 
+
+group the results according to the table they come from 
+
+add link to the table (change screen)
+
+//todo ; add a link in the record to the database record ..change which table is shown 
+
+//todo entity bionank  (id) ..make link to the screen 
+
+//clean up , by hand ..need some specialist  actually connect to an ontology , we have to options either we enter by hand and specialists correct them , or specialists add them  . 
+
+//todo : add a connection to concept wiki for each term (this link should be stored in termAccession.