[[PageOutline]]
== 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
* [http://hublog.hubmed.org/archives/001789.html UniProt / RDF / SPARQL]
* [http://labs.intellidimension.com/uniprot/default.rsp Experiments with Uniprot RDF and RDF Gateway]
* [http://dev.isb-sib.ch/projects/uniprot-rdf/migration.html#uniprot-r 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/
{{{
Thymic stromal lymphopoietin induces tight junction protein claudin-7 via NF-kappaB in dendritic cells.
Epithelial-derived thymic stromal lymphopoietin (TSLP) is an IL-7-like cytokine that triggers dendritic cell (DC)-mediated Th2-type inflammatory responses. ...
Kamekura, Ryuta
Kojima, Takashi
Takashima, Akira
Koizumi, Jun-Ichi
Ogasawara, Noriko
Go, Mitsuru
Takano, Ken-Ichi
Murata, Masaki
Tanaka, Satoshi
Ichimiya, Shingo
Himi, Tetsuo
Sawada, Norimasa
Histochem Cell Biol
2010-Jan-14
urn:issn:1432-119X
}}}
* dcterms
* prism
=== DBLP ===
== Rakefile ==
{{{
require 'open-uri'
require 'bio'
class Bio::MEDLINE
def subject_uri
""
end
def predicate(field)
""
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 ===
{{{
"10975656" .
"NLM" .
"MEDLINE" .
"20001211" .
"20010111" .
"20011128" .
"0894-0282 (Print)" .
"0894-0282 (Linking)" .
"13" .
"9" .
"2000 Sep" .
"Proteome analysis of differentially displayed proteins as a tool for the investigation of symbiosis." .
"995-1009" .
"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." .
"Plant-Microbe Interaction Group, Research School of Biological Sciences, Australian National University, Canberra City." .
"Natera, S H" .
"Guerreiro, N" .
"Djordjevic, M A" .
"Natera SH" .
"Guerreiro N" .
"Djordjevic MA" .
"eng" .
"Journal Article" .
"UNITED STATES" .
"Mol Plant Microbe Interact" .
"Molecular plant-microbe interactions : MPMI" .
"9107902" .
"0 (Proteome)" .
"7727-37-9 (Nitrogen)" .
"IM" .
"Electrophoresis, Gel, Two-Dimensional" .
"Fabaceae/*genetics/metabolism/microbiology" .
"Nitrogen/metabolism" .
"*Plants, Medicinal" .
"*Proteome" .
"Sinorhizobium meliloti/*genetics/metabolism" .
"Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization" .
"*Symbiosis" .
"2000/09/07" .
"2001/02/28" .
"2000/09/07" .
"10.1094/MPMI.2000.13.9.995 [doi]" .
"ppublish" .
"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
"Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization"
"Nitrogen/metabolism"
"*Symbiosis"
"*Plants, Medicinal"
"Electrophoresis, Gel, Two-Dimensional"
"Fabaceae/*genetics/metabolism/microbiology"
"*Proteome"
"Sinorhizobium meliloti/*genetics/metabolism"
"20010111"
"2000/09/07"
"10.1094/MPMI.2000.13.9.995 [doi]"
"9107902"
"2000/09/07"
"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."
"Djordjevic MA"
"Guerreiro N"
"Natera SH"
"20011128"
"UNITED STATES"
"0 (Proteome)"
"7727-37-9 (Nitrogen)"
"9"
"Molecular plant-microbe interactions : MPMI"
"NLM"
"2000 Sep"
"13"
"2001/02/28"
"Mol Plant Microbe Interact"
"995-1009"
"Plant-Microbe Interaction Group, Research School of Biological Sciences, Australian National University, Canberra City."
"ppublish"
"eng"
"Djordjevic, M A"
"Guerreiro, N"
"Natera, S H"
"0894-0282 (Print)"
"0894-0282 (Linking)"
"MEDLINE"
"20001211"
"IM"
"Journal Article"
}}}
mesh terms.
{{{
$ 4s-query pubmed -f text 'select * where { ?s ?mesh }' 10-01-13
?s ?mesh
"Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization"
"Nitrogen/metabolism"
"*Symbiosis"
"*Plants, Medicinal"
"Electrophoresis, Gel, Two-Dimensional"
"Fabaceae/*genetics/metabolism/microbiology"
"*Proteome"
"Sinorhizobium meliloti/*genetics/metabolism"
}}}
authors.
{{{
$ 4s-query pubmed -f text 'select * where { ?s ?au }' 10-01-13
?s ?au
"Djordjevic MA"
"Guerreiro N"
"Natera SH"
}}}
title.
{{{
$ 4s-query pubmed -f text 'select * where { ?s ?title }' 10-01-13
?s ?title
"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
{{{
10975656
2000
12
11
2001
01
11
2001
11
28
0894-0282
13
9
2000
Sep
Molecular plant-microbe interactions : MPMI
Mol. Plant Microbe Interact.
Proteome analysis of differentially displayed proteins as a tool for the investigation of symbiosis.
995-1009
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.
Plant-Microbe Interaction Group, Research School of Biological Sciences, Australian National University, Canberra City.
Natera
S H
SH
Guerreiro
N
N
Djordjevic
M A
MA
eng
Journal Article
UNITED STATES
Mol Plant Microbe Interact
9107902
0894-0282
0
Proteome
7727-37-9
Nitrogen
IM
Electrophoresis, Gel, Two-Dimensional
Fabaceae
genetics
metabolism
microbiology
Nitrogen
metabolism
Plants, Medicinal
Proteome
Sinorhizobium meliloti
genetics
metabolism
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Symbiosis
2000
9
7
11
0
2001
2
28
10
1
2000
9
7
11
0
ppublish
10975656
10.1094/MPMI.2000.13.9.995
}}}
== TogoWS RDF/Turtle ==
http://togows.dbcls.jp/entry/pubmed/10975656.ttl
A mixture of the simple but psuedo RDF (above) and the prism vocabulary.
* prism http://prismstandard.org/namespaces/1.2/basic/
{{{
"10975656" .
"pmid:10975656" .
.
"2000/09/07 11:00" .
"2000/09/07 11:00" .
"2001/02/28 10:01" .
"MEDLINE" .
"Proteome analysis of differentially displayed proteins as a tool for the investigation of symbiosis." .
"Proteome analysis of differentially displayed proteins as a tool for the investigation of symbiosis." .
"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." .
"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." .
"13" .
"13" .
"995-1009" .
"995" .
"2000 Sep" .
"" .
"" .
"Mol Plant Microbe Interact" .
"Mol Plant Microbe Interact" .
"Molecular plant-microbe interactions : MPMI" .
"Mol Plant Microbe Interact. 2000 Sep;13(9):995-1009." .
"IM" .
"Journal Article" .
"Natera, S H" .
"Natera, S H" .
"Guerreiro, N" .
"Guerreiro, N" .
"Djordjevic, M A" .
"Djordjevic, M A" .
"Natera SH" .
"Guerreiro N" .