EcoliWiki - User contributions [en]

The Arabidopsis Information Resource (TAIR)

2009-07-06T22:55:57Z

TanyaB: /* Discussion= */

{{Pagetop}}
[[Category:Databases]]
[[Category:MODs]]

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
http://www.arabidopsis.org/
|-
!align=left {{table heading style}} |What:
||
TAIR is the model organism database for Arabidopsis thaliana.
|-
!align=left {{table heading style}} |Who:
||

|-
!align=left {{table heading style}} |Updates:
||

|-
!align=left {{table heading style}} |Upcoming events:
||

|-
!align=left {{table heading style}} |Web Services:
||

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.1748.V4a24a37829d3e&page=1748&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[[Image:TAIR_home.jpg|right|Home Page|thumb|350px]]
[http://www.arabidopsis.org/ {{PAGENAME}}] is the model organism database for ''Arabidopsis thaliana'', providing integration of the available genomic data from the ''Arabidopsis'' community at large, as well as published literature and genome centers.

==Content==
TAIR encompasses information on the ''Arabidopsis'' genome with information on the genes, markers, polymorphisms, maps, sequences, clones, DNA, seed stocks, gene proteins and families, genome-wide expression data and biochemical pathways, as well as publications

== Using {{PAGENAME}}==
===Browsing===
Browsing TAIR is like any other site. There are plenty of links on the front page to direct the user's attention. The page header has the following categories: Advanced Search, Analysis Tools, Portals, FTP Downloads, ''Arabidopsis'' Information and Stocks. Each of these headings has a substantial number of sub-headings.

===Searching===
Searching TAIR seems to be straight-forward. There are two options for searching: either using the search bar on the main page, or clicking to the advanced search page.

There are several directions that one can search. For example, if one wanted to find information based on the gene Ku70, typing in Ku70 in the search bar and selecting Gene would pull-out the information on Ku70. Giving information on the Locus, gene model, a description of the gene, the full-length cDNA and keywords that are related to its [http://www.geneontology.org/ Gene Ontology Description]. Clicking on the Locus link pulls up the full page on the locus, including the ATG number, other names, the GO Annotations, any available RNA Data, Associated transcripts, the Chromosome it is located on and any predicted protein data (AA, Mw, IP,predicted domains).

There are additional, standard searches that can be done: searching by vector, sequences, microarray, and polymorphism/alleles.

Another nice search feature included in TAIR is the ability to search the ''Arabidopsis'' community by PI or lab. Searching for a researcher in the ''Arabidopsis'' field, if they are a registered user of TAIR, will pull-up the person's contact information, publications and affiliations. This is particularly nice because one can check a particular paper and see the annotations for the identified genes in that publication.

===Usage examples===
''Add links to additional pages describing success stories here.''

==Other sites with related content==
==Technology==
The TAIR website employs several tools for visualization, sequence analysis and data retrieval.
*[http://arabidopsis.org/servlets/mapper MapViewer:] MapViewer is a graphical interface for the integration of genetic, physical and sequence-based maps for each chromosome.

* [http://arabidopsis.org/servlets/sv SeqViewer] is the viewer for displaying gene annotation, clones, markers, transcripts and polymorphisms on the genome.

*[http://arabidopsis.org/Blast/ BLAST] tools are available at the site for searching against a variety of datasets.

*[http://arabidopsis.org/cgi-bin/fasta/nph-TAIRfasta.pl FASTA] for searching against a variety of datasets.

*[http://arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl PatMatch] was designed to identify short nucleotide and amino acid motifs using regular expressions for searching.

*[http://arabidopsis.org/tools/bulk Bulk data retrieval] allows users to retrieve large numbers of data.

*[http://arabidopsis.org/servlets/Order?state=search&mode=stock_number Ordering Stocks] is made easy with the collaboration with ABRC for the searching and ordering of stocks and strains from TAIR.

==Web Services/API==

==Discussion==

==References==
{{BacktoTop}}
{{RefHelp}}
<references />
'''TAIR: a resource for integrated ''Arabidoposis'' data''' 
Garcia-Hernandez ''et. al'' Functional Integrated Genomics (2002) 2:239-253 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed Abstract] [http://www.springerlink.com/(5poiie2bon3gxcuk2d3dtnm1)/app/home/contribution.asp?referrer=parent&backto=issue,1,7;journal,16,25;linkingpublicationresults,1:105695,1 Full-Text]
==External Links==
[http://www.arabidopsis.org/ {{PAGENAME}}]
===Discussion of {{PAGENAME}} on other websites===

The Arabidopsis Information Resource (TAIR)

2009-07-06T22:54:34Z

TanyaB: /* Web Services/API= */

{{Pagetop}}
[[Category:Databases]]
[[Category:MODs]]

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
http://www.arabidopsis.org/
|-
!align=left {{table heading style}} |What:
||
TAIR is the model organism database for Arabidopsis thaliana.
|-
!align=left {{table heading style}} |Who:
||

|-
!align=left {{table heading style}} |Updates:
||

|-
!align=left {{table heading style}} |Upcoming events:
||

|-
!align=left {{table heading style}} |Web Services:
||

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.1748.V4a24a37829d3e&page=1748&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[[Image:TAIR_home.jpg|right|Home Page|thumb|350px]]
[http://www.arabidopsis.org/ {{PAGENAME}}] is the model organism database for ''Arabidopsis thaliana'', providing integration of the available genomic data from the ''Arabidopsis'' community at large, as well as published literature and genome centers.

==Content==
TAIR encompasses information on the ''Arabidopsis'' genome with information on the genes, markers, polymorphisms, maps, sequences, clones, DNA, seed stocks, gene proteins and families, genome-wide expression data and biochemical pathways, as well as publications

== Using {{PAGENAME}}==
===Browsing===
Browsing TAIR is like any other site. There are plenty of links on the front page to direct the user's attention. The page header has the following categories: Advanced Search, Analysis Tools, Portals, FTP Downloads, ''Arabidopsis'' Information and Stocks. Each of these headings has a substantial number of sub-headings.

===Searching===
Searching TAIR seems to be straight-forward. There are two options for searching: either using the search bar on the main page, or clicking to the advanced search page.

There are several directions that one can search. For example, if one wanted to find information based on the gene Ku70, typing in Ku70 in the search bar and selecting Gene would pull-out the information on Ku70. Giving information on the Locus, gene model, a description of the gene, the full-length cDNA and keywords that are related to its [http://www.geneontology.org/ Gene Ontology Description]. Clicking on the Locus link pulls up the full page on the locus, including the ATG number, other names, the GO Annotations, any available RNA Data, Associated transcripts, the Chromosome it is located on and any predicted protein data (AA, Mw, IP,predicted domains).

There are additional, standard searches that can be done: searching by vector, sequences, microarray, and polymorphism/alleles.

Another nice search feature included in TAIR is the ability to search the ''Arabidopsis'' community by PI or lab. Searching for a researcher in the ''Arabidopsis'' field, if they are a registered user of TAIR, will pull-up the person's contact information, publications and affiliations. This is particularly nice because one can check a particular paper and see the annotations for the identified genes in that publication.

===Usage examples===
''Add links to additional pages describing success stories here.''

==Other sites with related content==
==Technology==
The TAIR website employs several tools for visualization, sequence analysis and data retrieval.
*[http://arabidopsis.org/servlets/mapper MapViewer:] MapViewer is a graphical interface for the integration of genetic, physical and sequence-based maps for each chromosome.

* [http://arabidopsis.org/servlets/sv SeqViewer] is the viewer for displaying gene annotation, clones, markers, transcripts and polymorphisms on the genome.

*[http://arabidopsis.org/Blast/ BLAST] tools are available at the site for searching against a variety of datasets.

*[http://arabidopsis.org/cgi-bin/fasta/nph-TAIRfasta.pl FASTA] for searching against a variety of datasets.

*[http://arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl PatMatch] was designed to identify short nucleotide and amino acid motifs using regular expressions for searching.

*[http://arabidopsis.org/tools/bulk Bulk data retrieval] allows users to retrieve large numbers of data.

*[http://arabidopsis.org/servlets/Order?state=search&mode=stock_number Ordering Stocks] is made easy with the collaboration with ABRC for the searching and ordering of stocks and strains from TAIR.

==Web Services/API==

=Discussion==

==References==
{{BacktoTop}}
{{RefHelp}}
<references />
'''TAIR: a resource for integrated ''Arabidoposis'' data''' 
Garcia-Hernandez ''et. al'' Functional Integrated Genomics (2002) 2:239-253 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed Abstract] [http://www.springerlink.com/(5poiie2bon3gxcuk2d3dtnm1)/app/home/contribution.asp?referrer=parent&backto=issue,1,7;journal,16,25;linkingpublicationresults,1:105695,1 Full-Text]
==External Links==
[http://www.arabidopsis.org/ {{PAGENAME}}]
===Discussion of {{PAGENAME}} on other websites===

The Arabidopsis Information Resource (TAIR)

2009-07-06T22:49:06Z

TanyaB: /* Technology */

{{Pagetop}}
[[Category:Databases]]
[[Category:MODs]]

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
http://www.arabidopsis.org/
|-
!align=left {{table heading style}} |What:
||
TAIR is the model organism database for Arabidopsis thaliana.
|-
!align=left {{table heading style}} |Who:
||

|-
!align=left {{table heading style}} |Updates:
||

|-
!align=left {{table heading style}} |Upcoming events:
||

|-
!align=left {{table heading style}} |Web Services:
||

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.1748.V4a24a37829d3e&page=1748&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[[Image:TAIR_home.jpg|right|Home Page|thumb|350px]]
[http://www.arabidopsis.org/ {{PAGENAME}}] is the model organism database for ''Arabidopsis thaliana'', providing integration of the available genomic data from the ''Arabidopsis'' community at large, as well as published literature and genome centers.

==Content==
TAIR encompasses information on the ''Arabidopsis'' genome with information on the genes, markers, polymorphisms, maps, sequences, clones, DNA, seed stocks, gene proteins and families, genome-wide expression data and biochemical pathways, as well as publications

== Using {{PAGENAME}}==
===Browsing===
Browsing TAIR is like any other site. There are plenty of links on the front page to direct the user's attention. The page header has the following categories: Advanced Search, Analysis Tools, Portals, FTP Downloads, ''Arabidopsis'' Information and Stocks. Each of these headings has a substantial number of sub-headings.

===Searching===
Searching TAIR seems to be straight-forward. There are two options for searching: either using the search bar on the main page, or clicking to the advanced search page.

There are several directions that one can search. For example, if one wanted to find information based on the gene Ku70, typing in Ku70 in the search bar and selecting Gene would pull-out the information on Ku70. Giving information on the Locus, gene model, a description of the gene, the full-length cDNA and keywords that are related to its [http://www.geneontology.org/ Gene Ontology Description]. Clicking on the Locus link pulls up the full page on the locus, including the ATG number, other names, the GO Annotations, any available RNA Data, Associated transcripts, the Chromosome it is located on and any predicted protein data (AA, Mw, IP,predicted domains).

There are additional, standard searches that can be done: searching by vector, sequences, microarray, and polymorphism/alleles.

Another nice search feature included in TAIR is the ability to search the ''Arabidopsis'' community by PI or lab. Searching for a researcher in the ''Arabidopsis'' field, if they are a registered user of TAIR, will pull-up the person's contact information, publications and affiliations. This is particularly nice because one can check a particular paper and see the annotations for the identified genes in that publication.

===Usage examples===
''Add links to additional pages describing success stories here.''

==Other sites with related content==
==Technology==
The TAIR website employs several tools for visualization, sequence analysis and data retrieval.
*[http://arabidopsis.org/servlets/mapper MapViewer:] MapViewer is a graphical interface for the integration of genetic, physical and sequence-based maps for each chromosome.

* [http://arabidopsis.org/servlets/sv SeqViewer] is the viewer for displaying gene annotation, clones, markers, transcripts and polymorphisms on the genome.

*[http://arabidopsis.org/Blast/ BLAST] tools are available at the site for searching against a variety of datasets.

*[http://arabidopsis.org/cgi-bin/fasta/nph-TAIRfasta.pl FASTA] for searching against a variety of datasets.

*[http://arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl PatMatch] was designed to identify short nucleotide and amino acid motifs using regular expressions for searching.

*[http://arabidopsis.org/tools/bulk Bulk data retrieval] allows users to retrieve large numbers of data.

*[http://arabidopsis.org/servlets/Order?state=search&mode=stock_number Ordering Stocks] is made easy with the collaboration with ABRC for the searching and ordering of stocks and strains from TAIR.

==Web Services/API===

=Discussion==

==References==
{{BacktoTop}}
{{RefHelp}}
<references />
'''TAIR: a resource for integrated ''Arabidoposis'' data''' 
Garcia-Hernandez ''et. al'' Functional Integrated Genomics (2002) 2:239-253 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed Abstract] [http://www.springerlink.com/(5poiie2bon3gxcuk2d3dtnm1)/app/home/contribution.asp?referrer=parent&backto=issue,1,7;journal,16,25;linkingpublicationresults,1:105695,1 Full-Text]
==External Links==
[http://www.arabidopsis.org/ {{PAGENAME}}]
===Discussion of {{PAGENAME}} on other websites===

The Arabidopsis Information Resource (TAIR)

2009-07-06T22:36:53Z

TanyaB: /* Searching */

{{Pagetop}}
[[Category:Databases]]
[[Category:MODs]]

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
http://www.arabidopsis.org/
|-
!align=left {{table heading style}} |What:
||
TAIR is the model organism database for Arabidopsis thaliana.
|-
!align=left {{table heading style}} |Who:
||

|-
!align=left {{table heading style}} |Updates:
||

|-
!align=left {{table heading style}} |Upcoming events:
||

|-
!align=left {{table heading style}} |Web Services:
||

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.1748.V4a24a37829d3e&page=1748&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[[Image:TAIR_home.jpg|right|Home Page|thumb|350px]]
[http://www.arabidopsis.org/ {{PAGENAME}}] is the model organism database for ''Arabidopsis thaliana'', providing integration of the available genomic data from the ''Arabidopsis'' community at large, as well as published literature and genome centers.

==Content==
TAIR encompasses information on the ''Arabidopsis'' genome with information on the genes, markers, polymorphisms, maps, sequences, clones, DNA, seed stocks, gene proteins and families, genome-wide expression data and biochemical pathways, as well as publications

== Using {{PAGENAME}}==
===Browsing===
Browsing TAIR is like any other site. There are plenty of links on the front page to direct the user's attention. The page header has the following categories: Advanced Search, Analysis Tools, Portals, FTP Downloads, ''Arabidopsis'' Information and Stocks. Each of these headings has a substantial number of sub-headings.

===Searching===
Searching TAIR seems to be straight-forward. There are two options for searching: either using the search bar on the main page, or clicking to the advanced search page.

There are several directions that one can search. For example, if one wanted to find information based on the gene Ku70, typing in Ku70 in the search bar and selecting Gene would pull-out the information on Ku70. Giving information on the Locus, gene model, a description of the gene, the full-length cDNA and keywords that are related to its [http://www.geneontology.org/ Gene Ontology Description]. Clicking on the Locus link pulls up the full page on the locus, including the ATG number, other names, the GO Annotations, any available RNA Data, Associated transcripts, the Chromosome it is located on and any predicted protein data (AA, Mw, IP,predicted domains).

There are additional, standard searches that can be done: searching by vector, sequences, microarray, and polymorphism/alleles.

Another nice search feature included in TAIR is the ability to search the ''Arabidopsis'' community by PI or lab. Searching for a researcher in the ''Arabidopsis'' field, if they are a registered user of TAIR, will pull-up the person's contact information, publications and affiliations. This is particularly nice because one can check a particular paper and see the annotations for the identified genes in that publication.

===Usage examples===
''Add links to additional pages describing success stories here.''

==Other sites with related content==
==Technology==
The TAIR website employs several tools for visulaization, sequence analysis and data retrieval.
*[http://arabidopsis.org/servlets/mapper MapViewer:] MapViewer is a graphical interface for the integration of genetic, physical and sequence-based maps for each chromosome.

* [http://arabidopsis.org/servlets/sv SeqViewer] is the viewer for displaying gene anootation, clones, markers, transcripts and polymorphisms on the genome.

*[http://arabidopsis.org/Blast/ BLAST] tools are available at the site for searching against a vaiety of datasets.

*[http://arabidopsis.org/cgi-bin/fasta/nph-TAIRfasta.pl FASTA] for searching against a vaiety of datasets.

*[http://arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl PatMatch] was designed to identify short nucleotide and amino acid motifs using regular expressions for searching.

*[http://arabidopsis.org/tools/bulk Bulk data retrieval] allows users to retrieve large numbers of data.

*[http://arabidopsis.org/servlets/Order?state=search&mode=stock_number Ordering Stocks] is made easy with the collaboration with ABRC for the searching and ordering of stocks and strains from TAIR.

==Web Services/API===

=Discussion==

==References==
{{BacktoTop}}
{{RefHelp}}
<references />
'''TAIR: a resource for integrated ''Arabidoposis'' data''' 
Garcia-Hernandez ''et. al'' Functional Integrated Genomics (2002) 2:239-253 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed Abstract] [http://www.springerlink.com/(5poiie2bon3gxcuk2d3dtnm1)/app/home/contribution.asp?referrer=parent&backto=issue,1,7;journal,16,25;linkingpublicationresults,1:105695,1 Full-Text]
==External Links==
[http://www.arabidopsis.org/ {{PAGENAME}}]
===Discussion of {{PAGENAME}} on other websites===

The Arabidopsis Information Resource (TAIR)

2009-07-06T22:31:46Z

TanyaB: /* Browsing */

{{Pagetop}}
[[Category:Databases]]
[[Category:MODs]]

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
http://www.arabidopsis.org/
|-
!align=left {{table heading style}} |What:
||
TAIR is the model organism database for Arabidopsis thaliana.
|-
!align=left {{table heading style}} |Who:
||

|-
!align=left {{table heading style}} |Updates:
||

|-
!align=left {{table heading style}} |Upcoming events:
||

|-
!align=left {{table heading style}} |Web Services:
||

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.1748.V4a24a37829d3e&page=1748&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[[Image:TAIR_home.jpg|right|Home Page|thumb|350px]]
[http://www.arabidopsis.org/ {{PAGENAME}}] is the model organism database for ''Arabidopsis thaliana'', providing integration of the available genomic data from the ''Arabidopsis'' community at large, as well as published literature and genome centers.

==Content==
TAIR encompasses information on the ''Arabidopsis'' genome with information on the genes, markers, polymorphisms, maps, sequences, clones, DNA, seed stocks, gene proteins and families, genome-wide expression data and biochemical pathways, as well as publications

== Using {{PAGENAME}}==
===Browsing===
Browsing TAIR is like any other site. There are plenty of links on the front page to direct the user's attention. The page header has the following categories: Advanced Search, Analysis Tools, Portals, FTP Downloads, ''Arabidopsis'' Information and Stocks. Each of these headings has a substantial number of sub-headings.

===Searching===
Searching TAIR Seems to be straight-forward. There are two options for searching: either using the search bar on the main page, or clicking to the advanced search page.

There are several directions that one can search. For example, if one wanted to find information based on the gene Ku70, typing in Ku70 in the bar and selecting Gene would pull-out the information on Ku70. Giving information on the Locus, gene model, a description of the gene, the full-length cDNA and keywords that are related to it's [http://www.geneontology.org/ Gene Ontology Description]. Clicking on the Locus link pulls up the full page on the locus, including the ATG number, other names, the GO Annotations, any available RNA Data, Associated transcripts, the Chromosome it is located on and any predicted protein data (AA, Mw, IP,predicted domains).

There are additional, standard searches that can be done: searching by vector, sequences, microarray, and polymorphism/alleles.

Another nice search feature included in TAIR is the ability to search the ''Arabidopsis'' community by PI or lab. Searching for a researcher in the ''Arabidopsis'' field, if they are a registered user of TAIR, will pull-up the person's contact information, publications and affiliations. This is particularly nice because one can check a particular paper and see the annotations for the identified genes in that publication.

===Usage examples===
''Add links to additional pages describing success stories here.''

==Other sites with related content==
==Technology==
The TAIR website employs several tools for visulaization, sequence analysis and data retrieval.
*[http://arabidopsis.org/servlets/mapper MapViewer:] MapViewer is a graphical interface for the integration of genetic, physical and sequence-based maps for each chromosome.

* [http://arabidopsis.org/servlets/sv SeqViewer] is the viewer for displaying gene anootation, clones, markers, transcripts and polymorphisms on the genome.

*[http://arabidopsis.org/Blast/ BLAST] tools are available at the site for searching against a vaiety of datasets.

*[http://arabidopsis.org/cgi-bin/fasta/nph-TAIRfasta.pl FASTA] for searching against a vaiety of datasets.

*[http://arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl PatMatch] was designed to identify short nucleotide and amino acid motifs using regular expressions for searching.

*[http://arabidopsis.org/tools/bulk Bulk data retrieval] allows users to retrieve large numbers of data.

*[http://arabidopsis.org/servlets/Order?state=search&mode=stock_number Ordering Stocks] is made easy with the collaboration with ABRC for the searching and ordering of stocks and strains from TAIR.

==Web Services/API===

=Discussion==

==References==
{{BacktoTop}}
{{RefHelp}}
<references />
'''TAIR: a resource for integrated ''Arabidoposis'' data''' 
Garcia-Hernandez ''et. al'' Functional Integrated Genomics (2002) 2:239-253 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed Abstract] [http://www.springerlink.com/(5poiie2bon3gxcuk2d3dtnm1)/app/home/contribution.asp?referrer=parent&backto=issue,1,7;journal,16,25;linkingpublicationresults,1:105695,1 Full-Text]
==External Links==
[http://www.arabidopsis.org/ {{PAGENAME}}]
===Discussion of {{PAGENAME}} on other websites===

The Arabidopsis Information Resource (TAIR)

2009-07-06T22:30:46Z

TanyaB: /* About {{PAGENAME}} */

{{Pagetop}}
[[Category:Databases]]
[[Category:MODs]]

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
http://www.arabidopsis.org/
|-
!align=left {{table heading style}} |What:
||
TAIR is the model organism database for Arabidopsis thaliana.
|-
!align=left {{table heading style}} |Who:
||

|-
!align=left {{table heading style}} |Updates:
||

|-
!align=left {{table heading style}} |Upcoming events:
||

|-
!align=left {{table heading style}} |Web Services:
||

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.1748.V4a24a37829d3e&page=1748&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[[Image:TAIR_home.jpg|right|Home Page|thumb|350px]]
[http://www.arabidopsis.org/ {{PAGENAME}}] is the model organism database for ''Arabidopsis thaliana'', providing integration of the available genomic data from the ''Arabidopsis'' community at large, as well as published literature and genome centers.

==Content==
TAIR encompasses information on the ''Arabidopsis'' genome with information on the genes, markers, polymorphisms, maps, sequences, clones, DNA, seed stocks, gene proteins and families, genome-wide expression data and biochemical pathways, as well as publications

== Using {{PAGENAME}}==
===Browsing===
Browsing TAIR is like any other site. There are plenty of links on the front page to direct the user's attention. The main page has headings of the following: Advanced Search, Analysis Tools, Portals, FTP Downloads, ''Arabidopsis'' Information and Stocks. Each of these headings has a substantial number of sub-headings.

===Searching===
Searching TAIR Seems to be straight-forward. There are two options for searching: either using the search bar on the main page, or clicking to the advanced search page.

There are several directions that one can search. For example, if one wanted to find information based on the gene Ku70, typing in Ku70 in the bar and selecting Gene would pull-out the information on Ku70. Giving information on the Locus, gene model, a description of the gene, the full-length cDNA and keywords that are related to it's [http://www.geneontology.org/ Gene Ontology Description]. Clicking on the Locus link pulls up the full page on the locus, including the ATG number, other names, the GO Annotations, any available RNA Data, Associated transcripts, the Chromosome it is located on and any predicted protein data (AA, Mw, IP,predicted domains).

There are additional, standard searches that can be done: searching by vector, sequences, microarray, and polymorphism/alleles.

Another nice search feature included in TAIR is the ability to search the ''Arabidopsis'' community by PI or lab. Searching for a researcher in the ''Arabidopsis'' field, if they are a registered user of TAIR, will pull-up the person's contact information, publications and affiliations. This is particularly nice because one can check a particular paper and see the annotations for the identified genes in that publication.

===Usage examples===
''Add links to additional pages describing success stories here.''

==Other sites with related content==
==Technology==
The TAIR website employs several tools for visulaization, sequence analysis and data retrieval.
*[http://arabidopsis.org/servlets/mapper MapViewer:] MapViewer is a graphical interface for the integration of genetic, physical and sequence-based maps for each chromosome.

* [http://arabidopsis.org/servlets/sv SeqViewer] is the viewer for displaying gene anootation, clones, markers, transcripts and polymorphisms on the genome.

*[http://arabidopsis.org/Blast/ BLAST] tools are available at the site for searching against a vaiety of datasets.

*[http://arabidopsis.org/cgi-bin/fasta/nph-TAIRfasta.pl FASTA] for searching against a vaiety of datasets.

*[http://arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl PatMatch] was designed to identify short nucleotide and amino acid motifs using regular expressions for searching.

*[http://arabidopsis.org/tools/bulk Bulk data retrieval] allows users to retrieve large numbers of data.

*[http://arabidopsis.org/servlets/Order?state=search&mode=stock_number Ordering Stocks] is made easy with the collaboration with ABRC for the searching and ordering of stocks and strains from TAIR.

==Web Services/API===

=Discussion==

==References==
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<references />
'''TAIR: a resource for integrated ''Arabidoposis'' data''' 
Garcia-Hernandez ''et. al'' Functional Integrated Genomics (2002) 2:239-253 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed Abstract] [http://www.springerlink.com/(5poiie2bon3gxcuk2d3dtnm1)/app/home/contribution.asp?referrer=parent&backto=issue,1,7;journal,16,25;linkingpublicationresults,1:105695,1 Full-Text]
==External Links==
[http://www.arabidopsis.org/ {{PAGENAME}}]
===Discussion of {{PAGENAME}} on other websites===