Changes between Initial Version and Version 1 of RDF/TogoWS/PubMed

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2011/02/16 18:05:08 (14 years ago)
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  • RDF/TogoWS/PubMed

    v1 v1  
     1== MEDLINE/PubMed data in RDF == 
     2 
     3MEDLINE/PubMed data spec. 
     4 * http://www.nlm.nih.gov/bsd/mms/medlineelements.html 
     5 
     6A PubMed entry URI 
     7 * http://togows.dbcls.jp/entry/pubmed/10975656 
     8 * http://pubmed.org/10975656 
     9 
     10Related works 
     11 * http://neurocommons.org/page/Bundles 
     12   *  http://neurocommons.org/page/Bundles/mesh/mesh-skos 
     13   * http://neurocommons.org/page/Bundles/mesh/qualified-headings 
     14   * http://neurocommons.org/page/Bundles/medline/subject-headings 
     15   * http://neurocommons.org/page/Bundles/medline/titles-years 
     16   * http://neurocommons.org/page/Bundles/ncbi/gene-pubmed 
     17   * http://neurocommons.org/page/Bundles/omim 
     18 * [http://hublog.hubmed.org/archives/001789.html UniProt / RDF / SPARQL]  
     19 * [http://labs.intellidimension.com/uniprot/default.rsp Experiments with Uniprot RDF and RDF Gateway] 
     20 * [http://dev.isb-sib.ch/projects/uniprot-rdf/migration.html#uniprot-r uniprot RDF :: Migration Guide] 
     21 
     22=== MEDLINE/PubMed record sample === 
     23{{{ 
     24PMID- 10975656 
     25OWN - NLM 
     26STAT- MEDLINE 
     27DA  - 20001211 
     28DCOM- 20010111 
     29LR  - 20011128 
     30IS  - 0894-0282 (Print) 
     31IS  - 0894-0282 (Linking) 
     32VI  - 13 
     33IP  - 9 
     34DP  - 2000 Sep 
     35TI  - Proteome analysis of differentially displayed proteins as a tool for the 
     36      investigation of symbiosis. 
     37PG  - 995-1009 
     38AB  - Two-dimensional gel electrophoresis was used to identify differentially 
     39      displayed proteins expressed during the symbiotic interaction between the 
     40      bacterium Sinorhizobium meliloti strain 1021 and the legume Melilotus alba 
     41      (white sweetclover). Our aim was to characterize novel symbiosis proteins 
     42      and to determine how the two symbiotic partners alter their respective 
     43      metabolisms as part of the interaction, by identifying gene products that 
     44      are differentially present between the symbiotic and non-symbiotic states. 
     45      Proteome maps from control M. alba roots, wild-type nodules, cultured S. 
     46      meliloti, and S. meliloti bacteroids were generated and compared. Over 250 
     47      proteins were induced or up-regulated in the nodule, compared with the 
     48      root, and over 350 proteins were down-regulated in the bacteroid form of 
     49      the rhizobia, compared with cultured cells. N-terminal amino acid 
     50      sequencing and matrix-assisted laser desorption/ionization time-of-flight 
     51      mass spectrometry peptide mass fingerprint analysis, in conjunction with 
     52      data base searching, were used to assign putative identity to nearly 100 
     53      nodule, bacterial, and bacteroid proteins. These included the previously 
     54      identified nodule proteins leghemoglobin and NifH as well as proteins 
     55      involved in carbon and nitrogen metabolism in S. meliloti. Bacteroid cells 
     56      showed down-regulation of several proteins involved in nitrogen 
     57      acquisition, including glutamine synthetase, urease, a urea-amide binding 
     58      protein, and a PII isoform, indicating that the bacteroids were nitrogen 
     59      proficient. The down-regulation of several enzymes involved in 
     60      polyhydroxybutyrate synthesis and a cell division protein was also 
     61      observed. This work shows that proteome analysis will be a useful strategy 
     62      to link sequence information and functional genomics. 
     63AD  - Plant-Microbe Interaction Group, Research School of Biological Sciences, 
     64      Australian National University, Canberra City. 
     65FAU - Natera, S H 
     66AU  - Natera SH 
     67FAU - Guerreiro, N 
     68AU  - Guerreiro N 
     69FAU - Djordjevic, M A 
     70AU  - Djordjevic MA 
     71LA  - eng 
     72PT  - Journal Article 
     73PL  - UNITED STATES 
     74TA  - Mol Plant Microbe Interact 
     75JT  - Molecular plant-microbe interactions : MPMI 
     76JID - 9107902 
     77RN  - 0 (Proteome) 
     78RN  - 7727-37-9 (Nitrogen) 
     79SB  - IM 
     80MH  - Electrophoresis, Gel, Two-Dimensional 
     81MH  - Fabaceae/*genetics/metabolism/microbiology 
     82MH  - Nitrogen/metabolism 
     83MH  - *Plants, Medicinal 
     84MH  - *Proteome 
     85MH  - Sinorhizobium meliloti/*genetics/metabolism 
     86MH  - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization 
     87MH  - *Symbiosis 
     88EDAT- 2000/09/07 
     89MHDA- 2001/02/28 
     90CRDT- 2000/09/07 
     91AID - 10.1094/MPMI.2000.13.9.995 [doi] 
     92PST - ppublish 
     93SO  - Mol Plant Microbe Interact. 2000 Sep;13(9):995-1009. 
     94}}} 
     95 
     96== Semantics annotation == 
     97=== gopubmed === 
     98http://gopubmed.org/  
     99{{{ 
     100<rdf:Description about="info:pmid/20077120"> 
     101<dc:title> 
     102Thymic stromal lymphopoietin induces tight junction protein claudin-7 via NF-kappaB in dendritic cells. 
     103</dc:title> 
     104<dcterms:abstract> 
     105Epithelial-derived thymic stromal lymphopoietin (TSLP) is an IL-7-like cytokine that triggers dendritic cell (DC)-mediated Th2-type inflammatory responses. ... 
     106</dcterms:abstract> 
     107<dcterms:creator>Kamekura, Ryuta</dcterms:creator> 
     108<dcterms:creator>Kojima, Takashi</dcterms:creator> 
     109<dcterms:creator>Takashima, Akira</dcterms:creator> 
     110<dcterms:creator>Koizumi, Jun-Ichi</dcterms:creator> 
     111<dcterms:creator>Ogasawara, Noriko</dcterms:creator> 
     112<dcterms:creator>Go, Mitsuru</dcterms:creator> 
     113<dcterms:creator>Takano, Ken-Ichi</dcterms:creator> 
     114<dcterms:creator>Murata, Masaki</dcterms:creator> 
     115<dcterms:creator>Tanaka, Satoshi</dcterms:creator> 
     116<dcterms:creator>Ichimiya, Shingo</dcterms:creator> 
     117<dcterms:creator>Himi, Tetsuo</dcterms:creator> 
     118<dcterms:creator>Sawada, Norimasa</dcterms:creator> 
     119<prism:publicationName>Histochem Cell Biol</prism:publicationName> 
     120<prism:publicationDate>2010-Jan-14</prism:publicationDate> 
     121<prism:publicationVolume/> 
     122<prism:isPartOf>urn:issn:1432-119X</prism:isPartOf> 
     123</rdf:Description> 
     124}}} 
     125 
     126 * dcterms 
     127 * prism 
     128 
     129=== DBLP === 
     130 
     131 
     132 
     133== Rakefile == 
     134{{{ 
     135require 'open-uri' 
     136require 'bio' 
     137 
     138class Bio::MEDLINE 
     139  def subject_uri 
     140    "<http://pubmed.org/#{self.pmid}>" 
     141  end 
     142  def predicate(field) 
     143    "<http://www.nlm.nih.gov/bsd/mms/medlineelements.html##{field.downcase}>"  
     144  end 
     145  def to_rdf 
     146    pubmed.keys.map do |field| 
     147      case field 
     148      when 'AU','FAU','MH','IS','RN' 
     149        self.pubmed[field].chomp.split("\n").map do |object| 
     150          [subject_uri, predicate(field), "\"#{object}\" ."].join("\t")  
     151        end 
     152      when 'AB','TI','AD' 
     153        [subject_uri, predicate(field), "\"#{self.pubmed[field].chomp.gsub("\n", ' ')}\" ."].join("\t")  
     154      else 
     155        [subject_uri, predicate(field), "\"#{self.pubmed[field].chomp}\" ."].join("\t")  
     156      end 
     157    end 
     158  end 
     159end 
     160 
     161desc 'test' 
     162task :test do 
     163  pm = open("http://togows.dbcls.jp/entry/pubmed/10975656").read 
     164  pm = Bio::MEDLINE.new(pm) 
     165  puts pm.to_rdf 
     166end 
     167}}} 
     168 
     169== Simple but psuedo RDF  == 
     170 * subjects: http://pubmed.org/${PMID} 
     171 * predicates: http://www.nlm.nih.gov/bsd/mms/medlineelements.html#${field_name} 
     172 * objects: Literal 
     173 
     174=== Convert task. === 
     175 
     176{{{ 
     177$ rake test -s > test.n3 
     178}}} 
     179 
     180 
     181=== test.n3 a PubMed in RDF === 
     182 
     183{{{ 
     184<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmid>      "10975656" . 
     185<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#own>       "NLM" . 
     186<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#stat>      "MEDLINE" . 
     187<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#da>        "20001211" . 
     188<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#dcom>      "20010111" . 
     189<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#lr>        "20011128" . 
     190<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#is>        "0894-0282 (Print)" . 
     191<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#is>        "0894-0282 (Linking)" . 
     192<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#vi>        "13" . 
     193<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#ip>        "9" . 
     194<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#dp>        "2000 Sep" . 
     195<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#ti>        "Proteome analysis of differentially displayed proteins as a tool for the investigation of symbiosis." . 
     196<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#pg>        "995-1009" . 
     197<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#ab>        "Two-dimensional gel electrophoresis was used to identify differentially displayed proteins expressed during the symbiotic interaction between the bacterium Sinorhizobium meliloti strain 1021 and the legume Melilotus alba (white sweetclover). Our aim was to characterize novel symbiosis proteins and to determine how the two symbiotic partners alter their respective metabolisms as part of the interaction, by identifying gene products that are differentially present between the symbiotic and non-symbiotic states. Proteome maps from control M. alba roots, wild-type nodules, cultured S. meliloti, and S. meliloti bacteroids were generated and compared. Over 250 proteins were induced or up-regulated in the nodule, compared with the root, and over 350 proteins were down-regulated in the bacteroid form of the rhizobia, compared with cultured cells. N-terminal amino acid sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry peptide mass fingerprint analysis, in conjunction with data base searching, were used to assign putative identity to nearly 100 nodule, bacterial, and bacteroid proteins. These included the previously identified nodule proteins leghemoglobin and NifH as well as proteins involved in carbon and nitrogen metabolism in S. meliloti. Bacteroid cells showed down-regulation of several proteins involved in nitrogen acquisition, including glutamine synthetase, urease, a urea-amide binding protein, and a PII isoform, indicating that the bacteroids were nitrogen proficient. The down-regulation of several enzymes involved in polyhydroxybutyrate synthesis and a cell division protein was also observed. This work shows that proteome analysis will be a useful strategy to link sequence information and functional genomics." . 
     198<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#ad>        "Plant-Microbe Interaction Group, Research School of Biological Sciences, Australian National University, Canberra City." . 
     199<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#fau>       "Natera, S H" . 
     200<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#fau>       "Guerreiro, N" . 
     201<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#fau>       "Djordjevic, M A" . 
     202<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#au>        "Natera SH" . 
     203<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#au>        "Guerreiro N" . 
     204<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#au>        "Djordjevic MA" . 
     205<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#la>        "eng" . 
     206<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#pt>        "Journal Article" . 
     207<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#pl>        "UNITED STATES" . 
     208<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#ta>        "Mol Plant Microbe Interact" . 
     209<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#jt>        "Molecular plant-microbe interactions : MPMI" . 
     210<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#jid>       "9107902" . 
     211<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#rn>        "0 (Proteome)" . 
     212<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#rn>        "7727-37-9 (Nitrogen)" . 
     213<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#sb>        "IM" . 
     214<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>        "Electrophoresis, Gel, Two-Dimensional" . 
     215<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>        "Fabaceae/*genetics/metabolism/microbiology" . 
     216<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>        "Nitrogen/metabolism" . 
     217<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>        "*Plants, Medicinal" . 
     218<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>        "*Proteome" . 
     219<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>        "Sinorhizobium meliloti/*genetics/metabolism" . 
     220<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>        "Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization" . 
     221<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>        "*Symbiosis" . 
     222<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#edat>      "2000/09/07" . 
     223<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mhda>      "2001/02/28" . 
     224<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#crdt>      "2000/09/07" . 
     225<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#aid>       "10.1094/MPMI.2000.13.9.995 [doi]" . 
     226<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#pst>       "ppublish" . 
     227<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#so>        "Mol Plant Microbe Interact. 2000 Sep;13(9):995-1009." . 
     228}}} 
     229 
     230 
     231 
     232=== Query and results === 
     233Store it into 4store. 
     234{{{ 
     235$ 4s-backend-setup pubmed 
     236$ 4s-backend pubmed 
     237$ 4s-import pubmed test.n3 
     238}}} 
     239 
     240Query. 
     241{{{ 
     242$ 4s-query pubmed -f text 'select * where { ?s ?p ?o }'  
     243?s      ?p      ?o 
     244 
     245<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>        "Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization" 
     246<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>        "Nitrogen/metabolism" 
     247<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>        "*Symbiosis" 
     248<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>        "*Plants, Medicinal" 
     249<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>        "Electrophoresis, Gel, Two-Dimensional" 
     250<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>        "Fabaceae/*genetics/metabolism/microbiology" 
     251<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>        "*Proteome" 
     252<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>        "Sinorhizobium meliloti/*genetics/metabolism" 
     253<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#dcom>      "20010111" 
     254<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#edat>      "2000/09/07" 
     255<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#aid>       "10.1094/MPMI.2000.13.9.995 [doi]" 
     256<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#jid>       "9107902" 
     257<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#crdt>      "2000/09/07" 
     258<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#ab>        "Two-dimensional gel electrophoresis was used to identify differentially displayed proteins expressed during the symbiotic interaction between the bacterium Sinorhizobium meliloti strain 1021 and the legume Melilotus alba (white sweetclover). Our aim was to characterize novel symbiosis proteins and to determine how the two symbiotic partners alter their respective metabolisms as part of the interaction, by identifying gene products that are differentially present between the symbiotic and non-symbiotic states. Proteome maps from control M. alba roots, wild-type nodules, cultured S. meliloti, and S. meliloti bacteroids were generated and compared. Over 250 proteins were induced or up-regulated in the nodule, compared with the root, and over 350 proteins were down-regulated in the bacteroid form of the rhizobia, compared with cultured cells. N-terminal amino acid sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry peptide mass fingerprint analysis, in conjunction with data base searching, were used to assign putative identity to nearly 100 nodule, bacterial, and bacteroid proteins. These included the previously identified nodule proteins leghemoglobin and NifH as well as proteins involved in carbon and nitrogen metabolism in S. meliloti. Bacteroid cells showed down-regulation of several proteins involved in nitrogen acquisition, including glutamine synthetase, urease, a urea-amide binding protein, and a PII isoform, indicating that the bacteroids were nitrogen proficient. The down-regulation of several enzymes involved in polyhydroxybutyrate synthesis and a cell division protein was also observed. This work shows that proteome analysis will be a useful strategy to link sequence information and functional genomics." 
     259<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#au>        "Djordjevic MA" 
     260<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#au>        "Guerreiro N" 
     261<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#au>        "Natera SH" 
     262<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#lr>        "20011128" 
     263<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#pl>        "UNITED STATES" 
     264<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#rn>        "0 (Proteome)" 
     265<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#rn>        "7727-37-9 (Nitrogen)" 
     266<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#ip>        "9" 
     267<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#jt>        "Molecular plant-microbe interactions : MPMI" 
     268<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#own>       "NLM" 
     269<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#dp>        "2000 Sep" 
     270<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#vi>        "13" 
     271<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mhda>      "2001/02/28" 
     272<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#ta>        "Mol Plant Microbe Interact" 
     273<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#pg>        "995-1009" 
     274<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#ad>        "Plant-Microbe Interaction Group, Research School of Biological Sciences, Australian National University, Canberra City." 
     275<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#pst>       "ppublish" 
     276<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#la>        "eng" 
     277<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#fau>       "Djordjevic, M A" 
     278<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#fau>       "Guerreiro, N" 
     279<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#fau>       "Natera, S H" 
     280<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#is>        "0894-0282 (Print)" 
     281<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#is>        "0894-0282 (Linking)" 
     282<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#stat>      "MEDLINE" 
     283<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#da>        "20001211" 
     284<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#sb>        "IM" 
     285<http://pubmed.org/10975656>    <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#pt>        "Journal Article" 
     286}}} 
     287 
     288mesh terms. 
     289{{{ 
     290$ 4s-query pubmed -f text 'select * where { ?s <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh> ?mesh }'                                                                                10-01-13 
     291?s      ?mesh 
     292<http://pubmed.org/10975656>    "Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization" 
     293<http://pubmed.org/10975656>    "Nitrogen/metabolism" 
     294<http://pubmed.org/10975656>    "*Symbiosis" 
     295<http://pubmed.org/10975656>    "*Plants, Medicinal" 
     296<http://pubmed.org/10975656>    "Electrophoresis, Gel, Two-Dimensional" 
     297<http://pubmed.org/10975656>    "Fabaceae/*genetics/metabolism/microbiology" 
     298<http://pubmed.org/10975656>    "*Proteome" 
     299<http://pubmed.org/10975656>    "Sinorhizobium meliloti/*genetics/metabolism" 
     300}}} 
     301 
     302authors. 
     303{{{ 
     304$ 4s-query pubmed -f text 'select * where { ?s <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#au> ?au }'                                                                                  10-01-13 
     305?s      ?au 
     306<http://pubmed.org/10975656>    "Djordjevic MA" 
     307<http://pubmed.org/10975656>    "Guerreiro N" 
     308<http://pubmed.org/10975656>    "Natera SH" 
     309}}} 
     310 
     311title. 
     312{{{ 
     313$ 4s-query pubmed -f text 'select * where { ?s <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#ti> ?title }'                                                                               10-01-13 
     314?s      ?title 
     315<http://pubmed.org/10975656>    "Proteome analysis of differentially displayed proteins as a tool for the investigation of symbiosis." 
     316}}} 
     317 
     318=== Issues === 
     319 1. Order of authors 
     320 2. Typing: Date, title, person, etc. 
     321 3. MeSH terms 
     322 4. subjects 
     323 
     324== Simple RDF from XML == 
     325 
     326=== MEDLINE Citation / PubMed Citation XML === 
     327  * http://www.nlm.nih.gov/news/medlinedata.html 
     328  * http://www.nlm.nih.gov/databases/dtd/ 
     329 
     330PMID:10975656 in the MedlineCitation XML 
     331{{{ 
     332<PubmedArticle> 
     333    <MedlineCitation Owner="NLM" Status="MEDLINE"> 
     334        <PMID>10975656</PMID> 
     335        <DateCreated> 
     336            <Year>2000</Year> 
     337            <Month>12</Month> 
     338            <Day>11</Day> 
     339        </DateCreated> 
     340        <DateCompleted> 
     341            <Year>2001</Year> 
     342            <Month>01</Month> 
     343            <Day>11</Day> 
     344        </DateCompleted> 
     345        <DateRevised> 
     346            <Year>2001</Year> 
     347            <Month>11</Month> 
     348            <Day>28</Day> 
     349        </DateRevised> 
     350        <Article PubModel="Print"> 
     351            <Journal> 
     352                <ISSN IssnType="Print">0894-0282</ISSN> 
     353                <JournalIssue CitedMedium="Print"> 
     354                    <Volume>13</Volume> 
     355                    <Issue>9</Issue> 
     356                    <PubDate> 
     357                        <Year>2000</Year> 
     358                        <Month>Sep</Month> 
     359                    </PubDate> 
     360                </JournalIssue> 
     361                <Title>Molecular plant-microbe interactions : MPMI</Title> 
     362                <ISOAbbreviation>Mol. Plant Microbe Interact.</ISOAbbreviation> 
     363            </Journal> 
     364            <ArticleTitle>Proteome analysis of differentially displayed proteins as a tool for the investigation of symbiosis.</ArticleTitle> 
     365            <Pagination> 
     366                <MedlinePgn>995-1009</MedlinePgn> 
     367            </Pagination> 
     368            <Abstract> 
     369                <AbstractText>Two-dimensional gel electrophoresis was used to identify differentially displayed proteins expressed during the symbiotic interaction between the bacterium Sinorhizobium meliloti strain 1021 and the legume Melilotus alba (white sweetclover). Our aim was to characterize novel symbiosis proteins and to determine how the two symbiotic partners alter their respective metabolisms as part of the interaction, by identifying gene products that are differentially present between the symbiotic and non-symbiotic states. Proteome maps from control M. alba roots, wild-type nodules, cultured S. meliloti, and S. meliloti bacteroids were generated and compared. Over 250 proteins were induced or up-regulated in the nodule, compared with the root, and over 350 proteins were down-regulated in the bacteroid form of the rhizobia, compared with cultured cells. N-terminal amino acid sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry peptide mass fingerprint analysis, in conjunction with data base searching, were used to assign putative identity to nearly 100 nodule, bacterial, and bacteroid proteins. These included the previously identified nodule proteins leghemoglobin and NifH as well as proteins involved in carbon and nitrogen metabolism in S. meliloti. Bacteroid cells showed down-regulation of several proteins involved in nitrogen acquisition, including glutamine synthetase, urease, a urea-amide binding protein, and a PII isoform, indicating that the bacteroids were nitrogen proficient. The down-regulation of several enzymes involved in polyhydroxybutyrate synthesis and a cell division protein was also observed. This work shows that proteome analysis will be a useful strategy to link sequence information and functional genomics.</AbstractText> 
     370            </Abstract> 
     371            <Affiliation>Plant-Microbe Interaction Group, Research School of Biological Sciences, Australian National University, Canberra City.</Affiliation> 
     372            <AuthorList CompleteYN="Y"> 
     373                <Author ValidYN="Y"> 
     374                    <LastName>Natera</LastName> 
     375                    <ForeName>S H</ForeName> 
     376                    <Initials>SH</Initials> 
     377                </Author> 
     378                <Author ValidYN="Y"> 
     379                    <LastName>Guerreiro</LastName> 
     380                    <ForeName>N</ForeName> 
     381                    <Initials>N</Initials> 
     382                </Author> 
     383                <Author ValidYN="Y"> 
     384                    <LastName>Djordjevic</LastName> 
     385                    <ForeName>M A</ForeName> 
     386                    <Initials>MA</Initials> 
     387                </Author> 
     388            </AuthorList> 
     389            <Language>eng</Language> 
     390            <PublicationTypeList> 
     391                <PublicationType>Journal Article</PublicationType> 
     392            </PublicationTypeList> 
     393        </Article> 
     394        <MedlineJournalInfo> 
     395            <Country>UNITED STATES</Country> 
     396            <MedlineTA>Mol Plant Microbe Interact</MedlineTA> 
     397            <NlmUniqueID>9107902</NlmUniqueID> 
     398            <ISSNLinking>0894-0282</ISSNLinking> 
     399        </MedlineJournalInfo> 
     400        <ChemicalList> 
     401            <Chemical> 
     402                <RegistryNumber>0</RegistryNumber> 
     403                <NameOfSubstance>Proteome</NameOfSubstance> 
     404            </Chemical> 
     405            <Chemical> 
     406                <RegistryNumber>7727-37-9</RegistryNumber> 
     407                <NameOfSubstance>Nitrogen</NameOfSubstance> 
     408            </Chemical> 
     409        </ChemicalList> 
     410        <CitationSubset>IM</CitationSubset> 
     411        <MeshHeadingList> 
     412            <MeshHeading> 
     413                <DescriptorName MajorTopicYN="N">Electrophoresis, Gel, Two-Dimensional</DescriptorName> 
     414            </MeshHeading> 
     415            <MeshHeading> 
     416                <DescriptorName MajorTopicYN="N">Fabaceae</DescriptorName> 
     417                <QualifierName MajorTopicYN="Y">genetics</QualifierName> 
     418                <QualifierName MajorTopicYN="N">metabolism</QualifierName> 
     419                <QualifierName MajorTopicYN="N">microbiology</QualifierName> 
     420            </MeshHeading> 
     421            <MeshHeading> 
     422                <DescriptorName MajorTopicYN="N">Nitrogen</DescriptorName> 
     423                <QualifierName MajorTopicYN="N">metabolism</QualifierName> 
     424            </MeshHeading> 
     425            <MeshHeading> 
     426                <DescriptorName MajorTopicYN="Y">Plants, Medicinal</DescriptorName> 
     427            </MeshHeading> 
     428            <MeshHeading> 
     429                <DescriptorName MajorTopicYN="Y">Proteome</DescriptorName> 
     430            </MeshHeading> 
     431            <MeshHeading> 
     432                <DescriptorName MajorTopicYN="N">Sinorhizobium meliloti</DescriptorName> 
     433                <QualifierName MajorTopicYN="Y">genetics</QualifierName> 
     434                <QualifierName MajorTopicYN="N">metabolism</QualifierName> 
     435            </MeshHeading> 
     436            <MeshHeading> 
     437                <DescriptorName MajorTopicYN="N">Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization</DescriptorName> 
     438            </MeshHeading> 
     439            <MeshHeading> 
     440                <DescriptorName MajorTopicYN="Y">Symbiosis</DescriptorName> 
     441            </MeshHeading> 
     442        </MeshHeadingList> 
     443    </MedlineCitation> 
     444    <PubmedData> 
     445        <History> 
     446            <PubMedPubDate PubStatus="pubmed"> 
     447                <Year>2000</Year> 
     448                <Month>9</Month> 
     449                <Day>7</Day> 
     450                <Hour>11</Hour> 
     451                <Minute>0</Minute> 
     452            </PubMedPubDate> 
     453            <PubMedPubDate PubStatus="medline"> 
     454                <Year>2001</Year> 
     455                <Month>2</Month> 
     456                <Day>28</Day> 
     457                <Hour>10</Hour> 
     458                <Minute>1</Minute> 
     459            </PubMedPubDate> 
     460            <PubMedPubDate PubStatus="entrez"> 
     461                <Year>2000</Year> 
     462                <Month>9</Month> 
     463                <Day>7</Day> 
     464                <Hour>11</Hour> 
     465                <Minute>0</Minute> 
     466            </PubMedPubDate> 
     467        </History> 
     468        <PublicationStatus>ppublish</PublicationStatus> 
     469        <ArticleIdList> 
     470            <ArticleId IdType="pubmed">10975656</ArticleId> 
     471            <ArticleId IdType="doi">10.1094/MPMI.2000.13.9.995</ArticleId> 
     472        </ArticleIdList> 
     473    </PubmedData> 
     474</PubmedArticle> 
     475}}} 
     476 
     477== TogoWS RDF/Turtle == 
     478http://togows.dbcls.jp/entry/pubmed/10975656.ttl 
     479 
     480A mixture of the simple but psuedo RDF (above) and the prism vocabulary. 
     481  * prism http://prismstandard.org/namespaces/1.2/basic/ 
     482{{{ 
     483<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#pmid>      "10975656" . 
     484<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://www.w3.org/2000/01/rdf-schema#label>    "pmid:10975656" .           
     485<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://purl.org/dc/elements/1.1/identifier>    <http://pubmed.org/10975656> . 
     486<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#crdt>      "2000/09/07 11:00" . 
     487<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#edat>      "2000/09/07 11:00" . 
     488<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#mhda>      "2001/02/28 10:01" . 
     489<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#stat>      "MEDLINE" . 
     490<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#ti>        "Proteome analysis of differentially displayed proteins as a tool for the investigation of symbiosis." . 
     491<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://purl.org/dc/elements/1.1/title> "Proteome analysis of differentially displayed proteins as a tool for the investigation of symbiosis." . 
     492<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#ab>        "Two-dimensional gel electrophoresis was used to identify differentially displayed proteins expressed during the symbiotic interaction between the bacterium Sinorhizobium meliloti strain 1021 and the legume Melilotus alba (white sweetclover). Our aim was to characterize novel symbiosis proteins and to determine how the two symbiotic partners alter their respective metabolisms as part of the interaction, by identifying gene products that are differentially present between the symbiotic and non-symbiotic states. Proteome maps from control M. alba roots, wild-type nodules, cultured S. meliloti, and S. meliloti bacteroids were generated and compared. Over 250 proteins were induced or up-regulated in the nodule, compared with the root, and over 350 proteins were down-regulated in the bacteroid form of the rhizobia, compared with cultured cells. N-terminal amino acid sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry peptide mass fingerprint analysis, in conjunction with data base searching, were used to assign putative identity to nearly 100 nodule, bacterial, and bacteroid proteins. These included the previously identified nodule proteins leghemoglobin and NifH as well as proteins involved in carbon and nitrogen metabolism in S. meliloti. Bacteroid cells showed down-regulation of several proteins involved in nitrogen acquisition, including glutamine synthetase, urease, a urea-amide binding protein, and a PII isoform, indicating that the bacteroids were nitrogen proficient. The down-regulation of several enzymes involved in polyhydroxybutyrate synthesis and a cell division protein was also observed. This work shows that proteome analysis will be a useful strategy to link sequence information and functional genomics." . 
     493<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://purl.org/dc/terms/abstract>     "Two-dimensional gel electrophoresis was used to identify differentially displayed proteins expressed during the symbiotic interaction between the bacterium Sinorhizobium meliloti strain 1021 and the legume Melilotus alba (white sweetclover). Our aim was to characterize novel symbiosis proteins and to determine how the two symbiotic partners alter their respective metabolisms as part of the interaction, by identifying gene products that are differentially present between the symbiotic and non-symbiotic states. Proteome maps from control M. alba roots, wild-type nodules, cultured S. meliloti, and S. meliloti bacteroids were generated and compared. Over 250 proteins were induced or up-regulated in the nodule, compared with the root, and over 350 proteins were down-regulated in the bacteroid form of the rhizobia, compared with cultured cells. N-terminal amino acid sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry peptide mass fingerprint analysis, in conjunction with data base searching, were used to assign putative identity to nearly 100 nodule, bacterial, and bacteroid proteins. These included the previously identified nodule proteins leghemoglobin and NifH as well as proteins involved in carbon and nitrogen metabolism in S. meliloti. Bacteroid cells showed down-regulation of several proteins involved in nitrogen acquisition, including glutamine synthetase, urease, a urea-amide binding protein, and a PII isoform, indicating that the bacteroids were nitrogen proficient. The down-regulation of several enzymes involved in polyhydroxybutyrate synthesis and a cell division protein was also observed. This work shows that proteome analysis will be a useful strategy to link sequence information and functional genomics." . 
     494<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#vi>        "13" . 
     495<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://prismstandard.org/namespaces/1.2/basic/volume>  "13" . 
     496<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#pg>        "995-1009" . 
     497<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://prismstandard.org/namespaces/1.2/basic/startingPage>    "995" . 
     498<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#dp>        "2000 Sep" . 
     499<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#dep>       "" . 
     500<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://prismstandard.org/namespaces/1.2/basic/publicationDate> "" . 
     501<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#ta>        "Mol Plant Microbe Interact" . 
     502<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://prismstandard.org/namespaces/1.2/basic/publicationName> "Mol Plant Microbe Interact" . 
     503<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#jt>        "Molecular plant-microbe interactions : MPMI" . 
     504<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#so>        "Mol Plant Microbe Interact. 2000 Sep;13(9):995-1009." . 
     505<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#sb>        "IM" . 
     506<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#pt>        "Journal Article" . 
     507<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#fau>       "Natera, S H" . 
     508<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://purl.org/dc/terms/creator>      "Natera, S H" . 
     509<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#fau>       "Guerreiro, N" . 
     510<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://purl.org/dc/terms/creator>      "Guerreiro, N" . 
     511<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#fau>       "Djordjevic, M A" . 
     512<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://purl.org/dc/terms/creator>      "Djordjevic, M A" . 
     513<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#au>        "Natera SH" . 
     514<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#au>        "Guerreiro N" . 
     515<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#au>        "Djordjevic MA" . 
     516<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#mh>        "Electrophoresis, Gel, Two-Dimensional" . 
     517<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#mh>        "Fabaceae/*genetics/metabolism/microbiology" . 
     518<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#mh>        "Nitrogen/metabolism" . 
     519<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#mh>        "*Plants, Medicinal" . 
     520<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#mh>        "*Proteome" . 
     521<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#mh>        "Sinorhizobium meliloti/*genetics/metabolism" . 
     522<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#mh>        "Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization" . 
     523<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#mh>        "*Symbiosis" . 
     524<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#jid>       "9107902" . 
     525<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#dcom>      "20010111" . 
     526<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#pst>       "ppublish" . 
     527<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#aid>       "10.1094/MPMI.2000.13.9.995 [doi]" . 
     528<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#pmc>       "" . 
     529<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#pl>        "UNITED STATES" . 
     530<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#lr>        "20011128" . 
     531<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#own>       "NLM" . 
     532<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#da>        "20001211" . 
     533<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#la>        "eng" . 
     534<http://togows.dbcls.jp/entry/ncbi-pubmed/10975656>     <http://togows.dbcls.jp/ontology/ncbi-pubmed#is>        "0894-0282 (Print) 0894-0282 (Linking)" . 
     535}}}