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
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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
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molgenis
inconsistencies in model--> annotate in ontology (additional validation??)
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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 )
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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
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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
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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)
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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.
