MEDLINE/PubMed data in RDF

MEDLINE/PubMed data spec.

•  http://www.nlm.nih.gov/bsd/mms/medlineelements.html

A PubMed? entry URI

•  http://togows.dbcls.jp/entry/pubmed/10975656
•  http://pubmed.org/10975656

Related works

•  http://neurocommons.org/page/Bundles
  •  http://neurocommons.org/page/Bundles/mesh/mesh-skos
  •  http://neurocommons.org/page/Bundles/mesh/qualified-headings
  •  http://neurocommons.org/page/Bundles/medline/subject-headings
  •  http://neurocommons.org/page/Bundles/medline/titles-years
  •  http://neurocommons.org/page/Bundles/ncbi/gene-pubmed
  •  http://neurocommons.org/page/Bundles/omim
•  UniProt / RDF / SPARQL
•  Experiments with Uniprot RDF and RDF Gateway
•  uniprot RDF :: Migration Guide

MEDLINE/PubMed record sample

PMID- 10975656
OWN - NLM
STAT- MEDLINE
DA  - 20001211
DCOM- 20010111
LR  - 20011128
IS  - 0894-0282 (Print)
IS  - 0894-0282 (Linking)
VI  - 13
IP  - 9
DP  - 2000 Sep
TI  - Proteome analysis of differentially displayed proteins as a tool for the
      investigation of symbiosis.
PG  - 995-1009
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.
AD  - Plant-Microbe Interaction Group, Research School of Biological Sciences,
      Australian National University, Canberra City.
FAU - Natera, S H
AU  - Natera SH
FAU - Guerreiro, N
AU  - Guerreiro N
FAU - Djordjevic, M A
AU  - Djordjevic MA
LA  - eng
PT  - Journal Article
PL  - UNITED STATES
TA  - Mol Plant Microbe Interact
JT  - Molecular plant-microbe interactions : MPMI
JID - 9107902
RN  - 0 (Proteome)
RN  - 7727-37-9 (Nitrogen)
SB  - IM
MH  - Electrophoresis, Gel, Two-Dimensional
MH  - Fabaceae/*genetics/metabolism/microbiology
MH  - Nitrogen/metabolism
MH  - *Plants, Medicinal
MH  - *Proteome
MH  - Sinorhizobium meliloti/*genetics/metabolism
MH  - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
MH  - *Symbiosis
EDAT- 2000/09/07
MHDA- 2001/02/28
CRDT- 2000/09/07
AID - 10.1094/MPMI.2000.13.9.995 [doi]
PST - ppublish
SO  - Mol Plant Microbe Interact. 2000 Sep;13(9):995-1009.

Semantics annotation

gopubmed

 http://gopubmed.org/

<rdf:Description about="info:pmid/20077120">
<dc:title>
Thymic stromal lymphopoietin induces tight junction protein claudin-7 via NF-kappaB in dendritic cells.
</dc:title>
<dcterms:abstract>
Epithelial-derived thymic stromal lymphopoietin (TSLP) is an IL-7-like cytokine that triggers dendritic cell (DC)-mediated Th2-type inflammatory responses. ...
</dcterms:abstract>
<dcterms:creator>Kamekura, Ryuta</dcterms:creator>
<dcterms:creator>Kojima, Takashi</dcterms:creator>
<dcterms:creator>Takashima, Akira</dcterms:creator>
<dcterms:creator>Koizumi, Jun-Ichi</dcterms:creator>
<dcterms:creator>Ogasawara, Noriko</dcterms:creator>
<dcterms:creator>Go, Mitsuru</dcterms:creator>
<dcterms:creator>Takano, Ken-Ichi</dcterms:creator>
<dcterms:creator>Murata, Masaki</dcterms:creator>
<dcterms:creator>Tanaka, Satoshi</dcterms:creator>
<dcterms:creator>Ichimiya, Shingo</dcterms:creator>
<dcterms:creator>Himi, Tetsuo</dcterms:creator>
<dcterms:creator>Sawada, Norimasa</dcterms:creator>
<prism:publicationName>Histochem Cell Biol</prism:publicationName>
<prism:publicationDate>2010-Jan-14</prism:publicationDate>
<prism:publicationVolume/>
<prism:isPartOf>urn:issn:1432-119X</prism:isPartOf>
</rdf:Description>

• dcterms
• prism

DBLP

Rakefile

require 'open-uri'
require 'bio'

class Bio::MEDLINE
  def subject_uri
    "<http://pubmed.org/#{self.pmid}>"
  end
  def predicate(field)
    "<http://www.nlm.nih.gov/bsd/mms/medlineelements.html##{field.downcase}>" 
  end
  def to_rdf
    pubmed.keys.map do |field|
      case field
      when 'AU','FAU','MH','IS','RN'
        self.pubmed[field].chomp.split("\n").map do |object|
          [subject_uri, predicate(field), "\"#{object}\" ."].join("\t") 
        end
      when 'AB','TI','AD'
        [subject_uri, predicate(field), "\"#{self.pubmed[field].chomp.gsub("\n", ' ')}\" ."].join("\t") 
      else
        [subject_uri, predicate(field), "\"#{self.pubmed[field].chomp}\" ."].join("\t") 
      end
    end
  end
end

desc 'test'
task :test do
  pm = open("http://togows.dbcls.jp/entry/pubmed/10975656").read
  pm = Bio::MEDLINE.new(pm)
  puts pm.to_rdf
end

Simple but psuedo RDF

• subjects:  http://pubmed.org/${PMID}
• predicates:  http://www.nlm.nih.gov/bsd/mms/medlineelements.html#${field_name}
• objects: Literal

Convert task.

$ rake test -s > test.n3

test.n3 a PubMed? in RDF

<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmid>	"10975656" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#own>	"NLM" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#stat>	"MEDLINE" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#da>	"20001211" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#dcom>	"20010111" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#lr>	"20011128" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#is>	"0894-0282 (Print)" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#is>	"0894-0282 (Linking)" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#vi>	"13" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#ip>	"9" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#dp>	"2000 Sep" .
<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." .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#pg>	"995-1009" .
<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." .
<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." .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#fau>	"Natera, S H" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#fau>	"Guerreiro, N" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#fau>	"Djordjevic, M A" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#au>	"Natera SH" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#au>	"Guerreiro N" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#au>	"Djordjevic MA" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#la>	"eng" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#pt>	"Journal Article" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#pl>	"UNITED STATES" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#ta>	"Mol Plant Microbe Interact" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#jt>	"Molecular plant-microbe interactions : MPMI" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#jid>	"9107902" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#rn>	"0 (Proteome)" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#rn>	"7727-37-9 (Nitrogen)" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#sb>	"IM" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>	"Electrophoresis, Gel, Two-Dimensional" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>	"Fabaceae/*genetics/metabolism/microbiology" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>	"Nitrogen/metabolism" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>	"*Plants, Medicinal" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>	"*Proteome" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>	"Sinorhizobium meliloti/*genetics/metabolism" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>	"Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>	"*Symbiosis" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#edat>	"2000/09/07" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mhda>	"2001/02/28" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#crdt>	"2000/09/07" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#aid>	"10.1094/MPMI.2000.13.9.995 [doi]" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#pst>	"ppublish" .
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#so>	"Mol Plant Microbe Interact. 2000 Sep;13(9):995-1009." .

Query and results

Store it into 4store.

$ 4s-backend-setup pubmed
$ 4s-backend pubmed
$ 4s-import pubmed test.n3

Query.

$ 4s-query pubmed -f text 'select * where { ?s ?p ?o }' 
?s	?p	?o

<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>	"Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>	"Nitrogen/metabolism"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>	"*Symbiosis"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>	"*Plants, Medicinal"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>	"Electrophoresis, Gel, Two-Dimensional"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>	"Fabaceae/*genetics/metabolism/microbiology"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>	"*Proteome"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh>	"Sinorhizobium meliloti/*genetics/metabolism"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#dcom>	"20010111"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#edat>	"2000/09/07"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#aid>	"10.1094/MPMI.2000.13.9.995 [doi]"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#jid>	"9107902"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#crdt>	"2000/09/07"
<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."
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#au>	"Djordjevic MA"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#au>	"Guerreiro N"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#au>	"Natera SH"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#lr>	"20011128"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#pl>	"UNITED STATES"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#rn>	"0 (Proteome)"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#rn>	"7727-37-9 (Nitrogen)"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#ip>	"9"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#jt>	"Molecular plant-microbe interactions : MPMI"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#own>	"NLM"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#dp>	"2000 Sep"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#vi>	"13"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mhda>	"2001/02/28"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#ta>	"Mol Plant Microbe Interact"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#pg>	"995-1009"
<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."
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#pst>	"ppublish"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#la>	"eng"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#fau>	"Djordjevic, M A"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#fau>	"Guerreiro, N"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#fau>	"Natera, S H"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#is>	"0894-0282 (Print)"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#is>	"0894-0282 (Linking)"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#stat>	"MEDLINE"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#da>	"20001211"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#sb>	"IM"
<http://pubmed.org/10975656>	<http://www.nlm.nih.gov/bsd/mms/medlineelements.html#pt>	"Journal Article"

mesh terms.

$ 4s-query pubmed -f text 'select * where { ?s <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#mh> ?mesh }'                                                                                10-01-13
?s	?mesh
<http://pubmed.org/10975656>	"Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization"
<http://pubmed.org/10975656>	"Nitrogen/metabolism"
<http://pubmed.org/10975656>	"*Symbiosis"
<http://pubmed.org/10975656>	"*Plants, Medicinal"
<http://pubmed.org/10975656>	"Electrophoresis, Gel, Two-Dimensional"
<http://pubmed.org/10975656>	"Fabaceae/*genetics/metabolism/microbiology"
<http://pubmed.org/10975656>	"*Proteome"
<http://pubmed.org/10975656>	"Sinorhizobium meliloti/*genetics/metabolism"

authors.

$ 4s-query pubmed -f text 'select * where { ?s <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#au> ?au }'                                                                                  10-01-13
?s	?au
<http://pubmed.org/10975656>	"Djordjevic MA"
<http://pubmed.org/10975656>	"Guerreiro N"
<http://pubmed.org/10975656>	"Natera SH"

title.

$ 4s-query pubmed -f text 'select * where { ?s <http://www.nlm.nih.gov/bsd/mms/medlineelements.html#ti> ?title }'                                                                               10-01-13
?s	?title
<http://pubmed.org/10975656>	"Proteome analysis of differentially displayed proteins as a tool for the investigation of symbiosis."

Issues

1. Order of authors
2. Typing: Date, title, person, etc.
3. MeSH terms
4. subjects

Simple RDF from XML

MEDLINE Citation / PubMed? Citation XML

•  http://www.nlm.nih.gov/news/medlinedata.html
•  http://www.nlm.nih.gov/databases/dtd/

PMID:10975656 in the MedlineCitation? XML

<PubmedArticle>
    <MedlineCitation Owner="NLM" Status="MEDLINE">
        <PMID>10975656</PMID>
        <DateCreated>
            <Year>2000</Year>
            <Month>12</Month>
            <Day>11</Day>
        </DateCreated>
        <DateCompleted>
            <Year>2001</Year>
            <Month>01</Month>
            <Day>11</Day>
        </DateCompleted>
        <DateRevised>
            <Year>2001</Year>
            <Month>11</Month>
            <Day>28</Day>
        </DateRevised>
        <Article PubModel="Print">
            <Journal>
                <ISSN IssnType="Print">0894-0282</ISSN>
                <JournalIssue CitedMedium="Print">
                    <Volume>13</Volume>
                    <Issue>9</Issue>
                    <PubDate>
                        <Year>2000</Year>
                        <Month>Sep</Month>
                    </PubDate>
                </JournalIssue>
                <Title>Molecular plant-microbe interactions : MPMI</Title>
                <ISOAbbreviation>Mol. Plant Microbe Interact.</ISOAbbreviation>
            </Journal>
            <ArticleTitle>Proteome analysis of differentially displayed proteins as a tool for the investigation of symbiosis.</ArticleTitle>
            <Pagination>
                <MedlinePgn>995-1009</MedlinePgn>
            </Pagination>
            <Abstract>
                <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>
            </Abstract>
            <Affiliation>Plant-Microbe Interaction Group, Research School of Biological Sciences, Australian National University, Canberra City.</Affiliation>
            <AuthorList CompleteYN="Y">
                <Author ValidYN="Y">
                    <LastName>Natera</LastName>
                    <ForeName>S H</ForeName>
                    <Initials>SH</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Guerreiro</LastName>
                    <ForeName>N</ForeName>
                    <Initials>N</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Djordjevic</LastName>
                    <ForeName>M A</ForeName>
                    <Initials>MA</Initials>
                </Author>
            </AuthorList>
            <Language>eng</Language>
            <PublicationTypeList>
                <PublicationType>Journal Article</PublicationType>
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            <Country>UNITED STATES</Country>
            <MedlineTA>Mol Plant Microbe Interact</MedlineTA>
            <NlmUniqueID>9107902</NlmUniqueID>
            <ISSNLinking>0894-0282</ISSNLinking>
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            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>Proteome</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>7727-37-9</RegistryNumber>
                <NameOfSubstance>Nitrogen</NameOfSubstance>
            </Chemical>
        </ChemicalList>
        <CitationSubset>IM</CitationSubset>
        <MeshHeadingList>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Electrophoresis, Gel, Two-Dimensional</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Fabaceae</DescriptorName>
                <QualifierName MajorTopicYN="Y">genetics</QualifierName>
                <QualifierName MajorTopicYN="N">metabolism</QualifierName>
                <QualifierName MajorTopicYN="N">microbiology</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Nitrogen</DescriptorName>
                <QualifierName MajorTopicYN="N">metabolism</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="Y">Plants, Medicinal</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="Y">Proteome</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Sinorhizobium meliloti</DescriptorName>
                <QualifierName MajorTopicYN="Y">genetics</QualifierName>
                <QualifierName MajorTopicYN="N">metabolism</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="Y">Symbiosis</DescriptorName>
            </MeshHeading>
        </MeshHeadingList>
    </MedlineCitation>
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                <Month>9</Month>
                <Day>7</Day>
                <Hour>11</Hour>
                <Minute>0</Minute>
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            <PubMedPubDate PubStatus="medline">
                <Year>2001</Year>
                <Month>2</Month>
                <Day>28</Day>
                <Hour>10</Hour>
                <Minute>1</Minute>
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                <Hour>11</Hour>
                <Minute>0</Minute>
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        <PublicationStatus>ppublish</PublicationStatus>
        <ArticleIdList>
            <ArticleId IdType="pubmed">10975656</ArticleId>
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