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.