Changes between Version 1 and Version 2 of OpenBio

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Timestamp:
2010/02/09 10:36:35 (8 years ago)
Author:
ktym
Comment:

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  • OpenBio

    v1 v2  
    1 = Open Bio* library = 
     1= Open Bio* Semantic Web tools = 
    22 
    3 == RDF libraries in each language == 
     3== Participants == 
    44 
    5 == Tools to manipulate RDF data == 
     5(Please add your name!) 
     6 
     7 * Toshiaki Katayama 
     8 
     9=== RDF libraries in each language === 
     10 
     11(Please add other languages as well!) 
     12 
     13Name of the available libraries 
     14 
     15 * Ruby 
     16  * ActiveRDF: may depends on Rails 
     17 * Python 
     18  * librdf 
     19 * Perl 
     20  * RDF: generic RDF library 
     21  * ONTO-Perl: OBO centric 
     22 
     23Functionality 
     24 
     25 * RDF reader (in) 
     26 * RDF generator (out) 
     27 
     28|| language || in || out|| 
     29|| Ruby || ? || ? || 
     30|| Python || o || ? || 
     31|| Perl || o || ? || 
     32 
     33=== Tools to manipulate RDF data === 
     34 
     35 * RDF grep 
     36 * RDF diff 
     37 * RDF sort 
     38 * RDF uniq 
     39 * RDF wc (triple count) 
     40 * RDF cat (combine) 
     41 
     42 ** (most of) these commands will output RDF graph :) 
     43 ** "sort" before "diff" is better. 
     44 ** it would be great if "diff" can have an option to ignore "empty node" which can shift internal IDs even if the graphs are almost same. 
     45 
     46=== RDF converters === 
     47 
     48 * general: 
     49  * RDF --> JSON (for CoarchDB, mongoDB etc.) 
     50 * biological: 
     51  * Bio DB entries -> RDF (in BioRuby for TogoWS, for example) 
     52  * OBO <-> RDF (used in Cell Cycle Ontology because ".obo" file format is easy to read for human) 
     53 
     54=== Interface for SPARQL endpoint === 
     55 
     56Language availability 
     57 
     58|| Ruby || ? || 
     59|| Python || o || 
     60|| Perl || ? || 
     61|| Java || o || 
     62|| R || ? || 
    663 
    764 
    8  
    9 == Interface for SPARQL endpoint == 
    10