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


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Timestamp:
2010-11-11T10:43:05+01:00 (14 years ago)
Author:
antonak
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  • DespoinaLog/2010/11/10

    v1 v1  
     1= Symposium on biological/bioinformatics metadata capture formats =
     210 /11/2010 
     3
     4study capture symposium 
     5
     6(open software )
     7
     8i3cube (not biological point of view
     9
     10open bis
     11
     12labkey
     13
     14isa creator
     15
     16wikilims
     17
     18galaxy
     19
     20bioeclipse
     21
     22============================================
     23
     24sysmo db :
     25
     26sysmo.net
     27
     28system biology 
     29
     30accèss permissions! groups of (whitelist /black list)
     31
     32MIAME , MIAPE , isainfrustructure (tabular)
     33
     34els………….---> rightfield(free to download)  :tooling for annotation inside els => drop down micraaray analysis template retrieve ontology terms….---> back to excels --> 
     35
     36csvmagetab-->rdf (convert magetab/csv to rdf )(SIMIRAL WORK)
     37
     38sbml
     39
     40jerm
     41
     42sysmo-db.org
     43
     44========================================
     45
     46molgenis
     47
     48inconsistencies in model--> annotate in ontology (additional validation??) 
     49
     50==============================
     51
     52FDA director :
     53
     542 genotypes --> 2 diets 
     55
     56environment,vars
     57
     58….
     59
     60model : core model that can be admined by a user from wizards (ui)
     61
     62xls exporter
     63
     64development (reload css js or both in the ui )
     65
     66=========================================
     67
     68sequencing
     69
     70(report, statistics-maps-rwa data, output, )
     71
     72mappability  -->  quality measurement 
     73
     74there is a lims so basically the problem of storing and presenting the data and the analysis is a matter of admininstratation
     75
     76=============================
     77
     78proteomics
     79
     80samples--> depletion--> digestion --> analysis (sneaps, biomarker candidates)
     81
     82(preparation protocols, )
     83
     84mass spectrometer, raw data, sanders format and then processing(quantitative, peptide/protein identification 
     85
     86labeling, 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)
     87
     88the same problems apply in metabolomics. ( )
     89
     90wrap2d : nbbpp.nl/warp2d.html
     91
     92================discussion 
     93
     94rdf
     95
     96there are some components that can be exchanged . 
     97
     98plone  in python dbnp
     99
     100ruby on rails --> jrybu 
     101
     102===== 
     103
     104morris on data models : 
     105
     106experiences form various projects 
     107
     108like gen2phen 
     109
     110many models
     111
     112magetab,(idf, sdrf, )
     113
     114xgap, 
     115
     116pheno fuge magetab++
     117
     118isatabm chado, hl7 
     119
     120=======================
     121
     122linked data approach 
     123
     124computational experiment (modeling ) in rdf ?
     125
     126biordf  , 
     127
     128swobjects 
     129
     130create a spqrql endpoint 
     131
     132query rewrinting to sql and sparql 
     133
     134sourceforge……./apps/mediawiki/swobjects
     135
     136;
     137
     138mores attic object --> CHAINING buffered : if then else rules …..
     139
     140do you have an example that actually connects these different datasest in 15 ????
     141
     142h eirwnia ienia to to minebiotext douleuei mono me gene idss den mporeis na ta vreis .
     143
     144SADI -fy the components (AIDA 
     145
     146===================================
     147
     148Scientific discourse (harvard) data & experiment 
     149
     150swan,sioc: ontology fro social networking  
     151
     152OBi, Mo efo 
     153
     154!MyExperiment,
     155
     156AO (annotation)
     157
     158Build an application ontology to integrate  
     159
     160
     161= Next steps  =
     162(spqrql endpoint in the server (gbic) include d2rq application 
     163
     164after a talk with christie : try to connect with concept wiki . maybe each term in the 
     165
     166database (ontologyerm???0 with the corresponding  term  in concept wiki . 
     167
     168also we'll talk about this in the conference "connecting biobanks"     
     169
     170//todo : add a connection to concept wiki for each term. (this will be a next step in the bbmri wiki)
     171
     172=======================================
     173
     17410/11/2010
     175
     176Search results : 
     177
     178searching the name 
     179
     180search for
     181
     182acronym is working 
     183
     184description is working 
     185
     186so for lastName not working : is it included in configuration file? twice 
     187
     188remove one and then try lastname instead of !LastName
     189
     190So the last name is included in the index. : but cannot be found as 
     191
     192All : 1st (contacts_lastName)as !InsertFieldValue inserted in Indexstored,indexed,tokenized<contacts_lastName:[de Leeuw, Kroon]>
     193
     194TODO : 
     195
     196group the results according to the table they come from 
     197
     198add link to the table (change screen)
     199
     200//todo ; add a link in the record to the database record ..change which table is shown 
     201
     202//todo entity bionank  (id) ..make link to the screen 
     203
     204//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  . 
     205
     206//todo : add a connection to concept wiki for each term (this link should be stored in termAccession.