Changes between Version 1 and Version 2 of Data_exchange

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Timestamp:
2010/02/12 16:46:19 (13 years ago)
Author:
gmicklem
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  • Data_exchange

    v1 v2  
    22Wednesday 10th February p.m. - Room 516 
    33 
    4 Semantic Data Exchange 
    5  
    6 Gos Micklem 
    7 Richard Smith 
    8 James Taylor 
    9 Arek Kasprzyk 
    10 Soichi Ogishima 
    11 Brad Chapman 
    12 Christian Zmasek 
    13 Peter Cock 
    14 Hideyuki Morita 
    15 Ryosuke Ishiwata 
    16 Kei Ono 
    17 Shinobu Okamoto 
    18 Alberto Labarga 
    19  
    20 ------------------------------------------------------------------------------ 
    21 Discussion on possibilities/need for improving data exchange between 
    22 e.g. InterMine, Galaxy, BioMart, Cytoscape... 
     4''' Semantic Data Exchange''' 
     5 
     6 * Gos Micklem 
     7 * Richard Smith 
     8 * James Taylor 
     9 * Arek Kasprzyk 
     10 * Soichi Ogishima 
     11 * Brad Chapman 
     12 * Christian Zmasek 
     13 * Peter Cock 
     14 * Hideyuki Morita 
     15 * Ryosuke Ishiwata 
     16 * Kei Ono 
     17 * Shinobu Okamoto 
     18 * Alberto Labarga 
     19 
     20'''Discussion on possibilities/need for improving data exchange between 
     21e.g. InterMine, Galaxy, BioMart, Cytoscape...''' 
    2322 
    2423Would typing of arbitrary data exchange improve communication between 
     
    2726 
    2827 
    29 Current situation: 
     28'''Current situation:''' 
    3029 
    3130It was felt that the current situation wasn't so bad: however it would 
     
    4241   needed> 
    4342 
    44    Cytoscape (http://www.cytoscape.org)/BioMart: REST API used.  Perhaps SOAP would be better but 
     43   Cytoscape (http://www.cytoscape.org) & BioMart: REST API used.  Perhaps SOAP would be better but 
    4544   this still requires some development.  REST was fine for data 
    4645   retrieval. 
     
    141140large-scale users/providers can start to comply. 
    142141 
    143  
    144 Data exchange conclusions: 
    145 *** A namespace for file formats would be useful. 
    146  
    147 *** A namespace for column of tabular data would be useful.  Could 
     142'''Data exchange conclusions:''' 
     143 * A namespace for file formats would be useful. 
     144 
     145 * A namespace for column of tabular data would be useful.  Could 
    148146    also be used to describe data in other formats e.g. XML, though 
    149147    this could be rather verbose. 
    150 *** Investigate whether the above exist. 
     148 * Investigate whether the above exist. 
    151149    Ontology Lookup Service (http://www.ebi.ac.uk/ontology-lookup) 
    152150    and/orLife Science Resource Name Project (http://www.lsrn.org) 
    153151    applicable ? 
    154152 
    155 *** At the moment namespaces for columns is probably more important 
     153 * At the moment namespaces for columns is probably more important 
    156154    than URIs for each data element in a column. 
    157155 
    158 Agreed that worthwhile to pass URIs to describe columns.  Agreed that 
    159 arbitrary human-friendly names are also good. 
    160  
    161 *** Agreed to dump all BioMart/ InterMine column headings out, find 
     156 * Agreed that worthwhile to pass URIs to describe columns.  Agreed that 
     157  arbitrary human-friendly names are also good. 
     158 
     159 * Agreed to dump all BioMart/ InterMine column headings out, find 
    162160    the common/commonly-used ones and work on naming. 
    163161 
    164162 
    165163 
    166 ========== Discussion turned to genome builds: 
     164'''Discussion turned to genome builds:''' 
    167165 
    168166There is no-where to go to find out if entities/ coordinates come from 
     
    201199version. 
    202200 
    203 Genome version summary: 
    204 * Investigate whether is there a standard available for describing genome version * 
    205 * Consider whether to base naming on ensembl genome/ annotation versions * 
    206  
    207  
    208  
    209 =========== Thoughts on RDF: 
     201'''Genome version summary:''' 
     202 * Investigate whether is there a standard available for describing genome version 
     203 * Consider whether to base naming on ensembl genome/ annotation versions 
     204 
     205 
     206 
     207'''Thoughts on RDF:''' 
    210208 
    211209If everyone is expressing their data in RDF with a common underlying