Changes between Version 6 and Version 7 of TextMining

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Timestamp:
2010/02/10 23:32:39 (14 years ago)
Author:
alabarga
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  • TextMining

    v6 v7  
    22= Text Mining Task Force = 
    33 
     4== Group activities == 
     5 
     6 * TextMiningDayOne 
     7 * TextMiningDayTwo 
    48 
    59== Members == 
    … …  
    2731  * Interfaces 
    2832 
    29 == Ideas == 
    3033 
    31 ==== Reflect RDFa snippets ==== 
     34== Implementation == 
    3235 
    33 Idea 1 (interlaced with the text): 
    34 {{{ 
    35 <div xmlns:sioc="http://rdfs.org/sioc/ns#" typeof="sioc:Item"> 
    36 <span class='reflect_protein'><a rel="sioc:topic" resource="http://purl.uniprot.org/uniprot/P05113"></a>IL-5</span> 
    37 </div> 
    38 }}} 
     36  * Make reflect generate RDFa 
     37  * Query Whatizit and Reflect. Get the RDFa data 
     38  * Use RDFa distiller to get RDF 
     39  * Get Pubmed data from togows 
     40  * Get Uniprot data 
     41  * Deploy in Sesame 
     42  * Make queries 
     43  * Expose as linked data with Pubby 
    3944 
    40 Idea 2 (at the end of the document, non-redundant): 
    41 {{{ 
    42 <div xmlns:sioc="http://rdfs.org/sioc/ns#" typeof="sioc:Item"> 
    43 <span id='reflectEntity0'>9606.ENSP00000231454</span> 
    44 <a rel="sioc:topic" resource="http://purl.uniprot.org/uniprot/P05113"></a> 
    45 </div> 
    46 }}} 
    47  
    48 ==== Whatizit RDFa service ==== 
    49  
    50 IL-5 Example: 
    51 http://whatizit.neurocommons.org/index.py/text_query?pipeline=whatizitEBIMedDiseaseChemicals&query=IL-5&format=atag&max_results=10 
    52  
    53 Converted to Turtle: 
    54 http://www.w3.org/2007/08/pyRdfa/extract?uri=http://whatizit.neurocommons.org/index.py/text_query?pipeline=whatizitEBIMedDiseaseChemicals&query=IL-5&format=atag&max_results=10 
    55  
    56 This uses a W3 service (http://www.w3.org/2007/08/pyRdfa/extract) 
    57  
    58 == Existing related implementations == 
    59  
    60 ==== Uniprot RDF ==== 
    61  
    62  
    63  http://www.uniprot.org/uniprot/P12345.n4 
    64  
    65 {{{ 
    66  
    67 uniprot:P12345 
    68   rdf:type Protein 
    69   alternativeName  
    70     rdf:type Structured_Name 
    71     fullName "Transaminase A" 
    72   citation <http://purl.uniprot.org/citations/4030726> 
    73     rdf:type Journal_Citation 
    74     title  
    75       "Aspartate aminotransferase isozymes from rabbit liver. Purification  
    76        and properties." 
    77     author "Kuramitsu S." 
    78     author "Inoue K." 
    79     author "Kondo K." 
    80     author "Aki K." 
    81     author "Kagamiyama H." 
    82     skos:exactMatch <http://purl.uniprot.org/medline/85289123> 
    83     skos:exactMatch <http://purl.uniprot.org/pubmed/4030726> 
    84     date 1985 
    85     name "J. Biochem." 
    86     volume 97 
    87     pages "1337-1345" 
    88     +rdf:type Citation_Statement 
    89     +scope "PROTEIN SEQUENCE" 
    90     +context  
    91       rdf:type Tissue 
    92       rdfs:label "Liver" 
    93  
    94  
    95 }}} 
    96  
    97 ==== Pubmed RDF @ TogoWS ==== 
    98  
    99  http://togows.dbcls.jp/entry/pubmed/4030726.ttl 
    100  
    101 {{{ 
    102 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#pmid>    "4030726" . 
    103 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://www.w3.org/2000/01/rdf-schema#label>    "pmid:4030726" .           
    104 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://purl.org/dc/elements/1.1/title> "pmid:4030726" .           
    105 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://purl.org/dc/elements/1.1/identifier>    <http://pubmed.org/4030726> . 
    106 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#own>     "NLM" . 
    107 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#stat>    "MEDLINE" . 
    108 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#da>      "1985-10-09" . 
    109 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#dcom>    "1985-10-09" . 
    110 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#lr>      "2007-12-19" . 
    111 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#vi>      "97" . 
    112 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://prismstandard.org/namespaces/2.0/basic/volume>  "97" . 
    113 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#dp>      "1985 May" . 
    114 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://prismstandard.org/namespaces/2.0/basic/prism:publicationDate>   "1985-05" . 
    115 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#ti>      "Aspartate aminotransferase isozymes from rabbit liver. Purification and properties." . 
    116 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://purl.org/dc/elements/1.1/title> "Aspartate aminotransferase isozymes from rabbit liver. Purification and properties." . 
    117 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#pg>      "1337-45" . 
    118 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://prismstandard.org/namespaces/2.0/basic/startingPage>    "1337" . 
    119 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#ab>      "Cytosolic and mitochondrial isozymes of aspartate aminotransferase (L-aspartate:2-oxoglutarate aminotransferase [EC 2.6.1.1] ) were purified to homogeneity from rabbit liver. The rabbit liver isozymes were closely similar to the corresponding isozymes from other sources, including human heart, pig heart, chicken heart, and rat liver, in their molecular weights, absorption spectra, amino acid compositions, isoelectric points, and Michaelis constants for the substrates. The NH2-terminal amino acid sequences of rabbit liver isozymes were identified up to 30 residues, and showed some differences from those of the corresponding isozymes obtained from other animals so far studied." . 
    120 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#ad>      "" . 
    121 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#fau>     "Kuramitsu, S" . 
    122 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://purl.org/dc/terms/creator>      "Kuramitsu, S" . 
    123 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#fau>     "Inoue, K" . 
    124 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://purl.org/dc/terms/creator>      "Inoue, K" . 
    125 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#fau>     "Kondo, K" . 
    126 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://purl.org/dc/terms/creator>      "Kondo, K" . 
    127 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#fau>     "Aki, K" . 
    128 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://purl.org/dc/terms/creator>      "Aki, K" . 
    129 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#fau>     "Kagamiyama, H" . 
    130 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://purl.org/dc/terms/creator>      "Kagamiyama, H" . 
    131 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#au>      "Kuramitsu S" . 
    132 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#au>      "Inoue K" . 
    133 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#au>      "Kondo K" . 
    134 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#au>      "Aki K" . 
    135 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#au>      "Kagamiyama H" . 
    136 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#pt>      "Journal Article Research Support, Non-U.S. Gov't" . 
    137 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#pl>      "JAPAN" . 
    138 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#ta>      "J Biochem" . 
    139 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://prismstandard.org/namespaces/2.0/basic/publicationName> "J Biochem" . 
    140 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#jt>      "Journal of biochemistry" . 
    141 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#jid>     "0376600" . 
    142 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#rn>      "0 (Isoenzymes)" . 
    143 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#sb>      "IM" . 
    144 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#mh>      "Amino Acid Sequence" . 
    145 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#mh>      "Amino Acids/analysis" . 
    146 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#mh>      "Animals" . 
    147 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#mh>      "Aspartate Aminotransferases/*isolation & purification/metabolism" . 
    148 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#mh>      "Isoelectric Point" . 
    149 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#mh>      "Isoenzymes/*isolation & purification/metabolism" . 
    150 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#mh>      "Kinetics" . 
    151 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#mh>      "Liver/*enzymology" . 
    152 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#mh>      "Molecular Weight" . 
    153 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#mh>      "Rabbits" . 
    154 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#mh>      "Spectrum Analysis" . 
    155 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#edat>    "1985-05-01" . 
    156 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#mhda>    "1985-05-01 00:01" . 
    157 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#crdt>    "1985-05-01 00:00" . 
    158 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#pst>     "ppublish" . 
    159 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#so>      "J Biochem. 1985 May;97(5):1337-45." . 
    160 <http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>      <http://togows.dbcls.jp/ns/ncbi-pubmed#la>      "eng" . 
    161  
    162 }}} 
    163  
    164 ==== Pubmed Linked Data @bio2rf ==== 
    165  
    166 http://bio2rdf.org/citations:4030726 
    167  
    168 {{{ 
    169  
    170 http://bio2rdf.org/citations:4030726     
    171        http://bio2rdf.org/bio2rdf_resource:linkedToFrom          
    172                 http://bio2rdf.org/uniprot:P12343 
    173                 http://bio2rdf.org/uniprot:P12343_1 
    174                 http://bio2rdf.org/uniprot:P12343_10 
    175                 http://bio2rdf.org/uniprot:P12343_6 
    176                 http://bio2rdf.org/uniprot:P12345 
    177                 http://bio2rdf.org/uniprot:P12345_1 
    178                 http://bio2rdf.org/uniprot:P12345_A 
    179         http://bio2rdf.org/bio2rdf_resource:url http://bio2rdf.org/html/citations:4030726 (Non-RDF URI) 
    180         http://creativecommons.org/ns#license   http://bio2rdf.org/license/citations:4030726 
    181         http://purl.uniprot.org/core/author      
    182                 Aki K. 
    183                 Inoue K. 
    184                 Kagamiyama H. 
    185                 Kondo K. 
    186                 Kuramitsu S. 
    187         http://purl.uniprot.org/core/date       1985 
    188         http://purl.uniprot.org/core/name       J. Biochem. 
    189         http://purl.uniprot.org/core/pages      1337-1345 
    190         http://purl.uniprot.org/core/title      Aspartate aminotransferase isozymes from rabbit liver. Purification and properties. 
    191         http://purl.uniprot.org/core/volume     97 
    192         http://www.w3.org/1999/02/22-rdf-syntax-ns#type         http://bio2rdf.org/core:Journal_Citation 
    193         http://www.w3.org/2002/07/owl#sameAs    http://bio2rdf.org/medline:85289123  
    194                                                 http://bio2rdf.org/pubmed:4030726 
    195  
    196 }}}