Difference between revisions of "Links to sites using the PO"

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[http://www.agbase.msstate.edu/ AgBase]
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=Ontology Listing Services, etc=
 +
[http://agroportal.lirmm.fr/ Agroportal]
 +
 
 +
[http://bioportal.bioontology.org/ Bioportal]
 +
 
 +
[http://www.cropontology.org/ Crop Ontology]- PO is listed along with the crop-specific onotlogies
 +
 
 +
[http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PO EBI OLS]
 +
 
 +
[http://www.obofoundry.org/ OBO Foundry]
 +
 
 +
[http://ontofox.hegroup.org/ OntoFox]- web-based Ontology tool that fetches ontology terms and axioms
 +
 
 +
[http://www.ontobee.org/ OntoBee]- A linked data server designed for ontologies, the goal is to facilitate ontology data sharing, visualization, query, integration, and analysis.
 +
 
 +
[http://isatab.sourceforge.net/ ISA Tools Software Suite]- Use of ontologies is recommended
 +
 
 +
[http://www.metabolomics-msi.org/ Metabolomics Standards Initiative]- PO is recommended in MSI standards
 +
 
 +
[https://www.agbiodata.org/ AgBioData Site]- Consortium of agricultural biological databases and associated resources
 +
 
 +
=A to F=
 +
[https://www.ebi.ac.uk/fg/annotare/ Annotare]- Array Express experiment submission tool- supports an ontology widget that is enabled with ontology look-up services of the NCBO Bioportal
 +
 
 +
* Ref: [https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btq462 Annotare—a tool for annotating high-throughput biomedical investigations and resulting data] Bioinformatics, Volume 26, Issue 19, 1 October 2010, Pages 2470–2471
 +
 
 +
[https://arapheno.1001genomes.org/ontology/PTO/ Arapheno] - search by TO or EO, weird versions
 +
 
 +
[https://bip.earlham.ac.uk/ Brassica Information Portal] - TO and PO terms can be used to search, have requested new terms ([https://github.com/Planteome/plant-trait-ontology/issues/391 #391] and [https://github.com/Planteome/plant-trait-ontology/issues/392 #392])
 +
 
 +
[http://www.brenda-enzymes.info/ BRENDA]- Enzyme Database, mostly uses BTO, but old version of PO, TO and EO are on their Ontology explorer
  
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[https://database.riken.jp/sw/ ARTADE2DB]
 
  
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[http://www.brenda-enzymes.info/ BRENDA]
 
  
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Compositae Genomics Project: [http://compgenomics.ucdavis.edu/morphodb/analysis/viewOntology.php Morphdb]
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_______________________________________________________________________
  
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[http://www.cosmoss.org/ cosmoss]
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[http://www.agbase.msstate.edu/ AgBase]- only has annotations to GO
  
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[http://www.geneontology.org/ Gene Ontology]
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[https://database.riken.jp/sw/ ARTADE2DB]- link not working?
  
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[http://www.gramene.org/plant_ontology/ Gramene]
+
[http://biolod.org/ Biolod.org] example page: [http://biolod.org/class/cria131u4510i/PO_0004510 non-secretory trichome]
 +
see also: [http://biolod.org/database/ria131i/PO_class_structure_Plant_structure plant structure] - site and links not working?
  
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[http://bioportal.bioontology.org/ Bioportal]
+
[http://brassibase.cos.uni-heidelberg.de/ Brassibase]- No PO on their site
 +
 
 +
[http://www.cosmoss.org/ cosmoss]- No PO on their site
 +
 
 +
[http://www.cyverse.org/ Cyverse]- mirror site of planteome, otherwise not sure how it is being used
 +
 
 +
=G to L=
 +
 
 +
[http://archive.gramene.org/plant_ontology/ Gramene Archive]- Old ontology browsers, can browse PO, TO, PECO, and GO
 +
 
 +
[http://ensembl.gramene.org/biomart/martview/a5af63c60de7ebc805c5f558d7459deb Gramene Biomart]- can filter by PO and GO
 +
 
 +
[http://genomes.cribi.unipd.it/grape/ Grape genome database]
 +
 
 +
[http://genomes.cribi.unipd.it/cgi-bin/pqs2/query.pl?release=v1#Ontologies Query page CRIBI]- Grape genes are annotated to PO terms
 +
 
 +
_____________________________________________________________________________________________________________
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 +
[http://www.geneontology.org/ Gene Ontology]- No PO or TO?
 +
 
 +
[https://sites.google.com/site/liveplantimagegroup/home Live Plant Image Group]- has links to browse PO, but not sure how it is used
 +
 
 +
=M to P=
 +
 
 +
[http://bioinformatics.intec.ugent.be/magic/ MAGIC]- 'MAize Gene expressIon Compendium'- a web-based interface for exploring and analyzing a comprehensive maize-specific cross-platform expression compendium.
 +
 
 +
* This compendium was constructed by collecting, homogenizing and formally annotating publicly available microarrays from Gene Expression Omnibus (GEO), and ArrayExpress. Includes plant ontology annotations
 +
 
 +
* REF: [https://academic.oup.com/bioinformatics/article/30/9/1316/234066/MAGIC-access-portal-to-a-cross-platform-gene MAGIC: access portal to a cross-platform gene expression compendium for maize]-  Fu et al (2014), Bioinformatics. doi: 10.1093/bioinformatics/btt739
 +
 
 +
[http://maizegdb.org/gene_center/gene/GRMZM2G119578 MaizeGDB Genes]- PO annotations are listed on Gene pages from Sekhon study.
  
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[http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PO EBI OLS]
+
[http://maize.jcvi.org/cellgenomics/ecell.php?search=10 Maize cell Genomics database]- images tagged with PO ids
  
 +
[http://www.genomeindia.org/biocuration/ Manually Curated Database of Rice Proteins]- Data is tagged with PO, TO and PECO terms
  
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[http://www.iplantcollaborative.org/ iplant]
+
[http://services.cbib.u-bordeaux2.fr/MERYB/vocabulary/ontology.php?section=2&sel=&expand=1&term_id=603&specie= Metabolomic Repository Bordeaux MeRy]- plant metabolomics platform allowing the storage and visualisation of Nuclear Magnetic Resonance (NMR) metabolic profiles from plants, but has old version of PO and EO
  
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[https://sites.google.com/site/liveplantimagegroup/home Live Plant Image Group]
+
[http://compgenomics.ucdavis.edu/morphodb/analysis/viewOntology.php The Compositae Genome Project (CGP)]- Morphodb Cool PO browser with links to annotated data from lettuce and sunflower, really old version of PO
  
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[http://arabidopsis.info/cgi-bin/ontology/nasc_po/go.cgi?search_constraint=terms&action=replace_tree&session_id=8730b1287179734 NASC Ontology page]
+
[http://shigen.nig.ac.jp/plantontology/ja/go Oryzabase PO Version ]- Japanese version of old PO (plant structures only translated)
  
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[http://www.cs.utexas.edu/~miranker/studentWeb/OntobrowserHomePage.html OntoBrowser]
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[http://bioweb.supagro.inra.fr/phenopsis/ Phenopsis] - from INRA, information system dedicated to the model plant Arabidopsis thaliana; ontology terms are out of date on here, links go go to the EBI OLS
 +
* see page: [http://bioweb.supagro.inra.fr/phenopsis/ConsulterOrgane.php PO terms]
  
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[http://ontofox.hegroup.org/ OntoFox]
+
[http://caps.ncbs.res.in/poeas/index.html POEAS]- Plant Ontology Enrichment Analysis Server, automated Plant Phenomic Analysis Using Plant Ontology terms based on genes from Arabidopsis thaliana
  
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[http://isatab.sourceforge.net/ ISA]
 
  
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[http://www.maizegdb.org/ MaizeGDB]
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[https://academic.oup.com/gigascience/article/5/1/1/2756883/Plant-specimen-contextual-data-consensus Plant-specimen-contextual-data-consensus]
  
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[http://www.metalife.com/index.html Metalife]
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_________________________________________________________________________________________________________
  
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[[PO integration in MSI standards]]
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[https://database.riken.jp/sw/en/Home/cria301u1i/ The Integrated Databases of Plant Omics Data]- link not working
  
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[http://www.obofoundry.org/ OBO Foundry]
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[http://www.cs.utexas.edu/~miranker/studentWeb/OntobrowserHomePage.html OntoBrowser]- interactive ontology navigator and ontology-based image retrieval system. It makes use of an ontology to retrieve images. page not loading...
  
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[http://www.ontobee.org/browser/index.php?o=PO OntoBee]
+
[http://biolod.org/database/ria224i/Plant_Phenome Plant Phenome]- on Biolod, links not functional
  
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[http://www.plantsystematics.org Plantsystematics.org]
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[http://arabidopsis.info/NASC NASC Ontology page]- link to ontology browser is not functional
  
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[[Phenopsis]]  
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[https://shigen.nig.ac.jp/rice/oryzabase/ Oryzabase]- no links to PO terms
  
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[http://semantic-json.org/sw/wiki/en/cria160s1ria160s5i/#applications Riken]
+
[http://www.plantsystematics.org Plantsystematics.org]- ?? cant find any PO ref
  
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[https://database.riken.jp/sw/en/Home/cria301u1i/ The Integrated Databases of Plant Omics Data]
+
[https://www.ebi.ac.uk/pride/archive/ PRIDE]- PRoteomics IDEntifications (PRIDE) database, used to have a ontology query, but cannot find it now
  
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[http://solgenomics.net/tools/onto/index.pl Solanaceae Genome network (SGN) ]
+
=R to Z=
  
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[http://traitnet.ecoinformatics.org/ Traitnet]
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[http://rarge-v2.psc.riken.jp/ RARGEII]- RIKEN Arabidopsis Genome Encyclopedia, Search mutant lines by phenotypes- use PO or PATO
  
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[http://www.uniprot.org/keywords/ Uniprot keywords] ???
+
[http://solgenomics.net/tools/onto/index.pl Solanaceae Genome network (SGN)]- can browse/search by GO,PO, SO, PATO
  
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[http://virtualplant.bio.nyu.edu/cgi-bin/vpweb/ Virtual plant]
+
[http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/phenotype.cgi?search=AP%3A0025099 SuperFamily Phenotype Browser]  
 +
* Prefix changed to AP - 'Arabidopsis Plant ontology' with 2 subontologies (PAN for Plant ANatomical entity, PDE for Plant structure DEvelopment stage), "AP:0025099" used here is equivalent to "PO:0025099" in original ontology
 +
* need to address some issues here, not an "Arabidopsis Plant Ontology"
  
−
[http://biolod.org/ Biolod.org]    example page: [http://biolod.org/class/cria131u4510i/PO_0004510 non-secretory trichome]
+
[http://virtualplant.bio.nyu.edu/cgi-bin/vpweb/ Virtual plant]- browse the Plant Ontology to see Arabidopsis genes annotated to that term
−
see also: [http://biolod.org/database/ria131i/PO_class_structure_Plant_structure plant structure]
 
  
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the PO is also featured here:  [http://biolod.org/database/ria224i/Plant_Phenome Plant Phenome]
+
[https://www.arabidopsis.org/ TAIR] - GO_and_PO_Annotations can be downloaded, browse by ontology terms
  
 +
[http://ist.blogs.inra.fr/wdi/ Wheat Data Interoperability Guidelines] - Recommendations prepared by the Wheat Data Interoperability Working Group, of the Research Data Alliance
  
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Others?
+
________________________________________________________________________________________________
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not actually using the PO but should be:
 
  
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[http://bar.utoronto.ca/welcome.htm Bio-Array Resource for Plant Biology (BAR)]
+
[https://soybase.org/ SoyBase]- AmiGO browser of Soy Ontology terms, not mapped to PO or TO- just to SOY ontology
  
−
Crop Ontology http://www.cropontology.org/
+
[http://traitnet.ecoinformatics.org/ Traitnet]- no ontology searches etc from their site...
  
 +
[http://www.uniprot.org/keywords/ Uniprot keywords]- can search for GO terms, no use of PO ??
  
−
[https://www.genevestigator.com/gv/plant.jsp Genevestigator]
+
=Others?=
 +
not actually using the PO but should be:
  
−
[http://genomics.cribi.unipd.it/Main_Page CRIBI] and the [http://genomes.cribi.unipd.it/cgi-bin/pqs2/query.pl?release=v1#Ontologies Query page]
+
[http://bar.utoronto.ca/welcome.htm Bio-Array Resource for Plant Biology (BAR)]  
  
−
[http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/phenotype.cgi?search=AP%3A0025099 SuperFamily] - need to address some issues here, not an "Arabidopsis Plant Ontology".
+
[https://www.genevestigator.com/gv/plant.jsp Genevestigator]

Latest revision as of 17:31, 5 September 2017

Ontology Listing Services, etc

Agroportal

Bioportal

Crop Ontology- PO is listed along with the crop-specific onotlogies

EBI OLS

OBO Foundry

OntoFox- web-based Ontology tool that fetches ontology terms and axioms

OntoBee- A linked data server designed for ontologies, the goal is to facilitate ontology data sharing, visualization, query, integration, and analysis.

ISA Tools Software Suite- Use of ontologies is recommended

Metabolomics Standards Initiative- PO is recommended in MSI standards

AgBioData Site- Consortium of agricultural biological databases and associated resources

A to F

Annotare- Array Express experiment submission tool- supports an ontology widget that is enabled with ontology look-up services of the NCBO Bioportal

Arapheno - search by TO or EO, weird versions

Brassica Information Portal - TO and PO terms can be used to search, have requested new terms (#391 and #392)

BRENDA- Enzyme Database, mostly uses BTO, but old version of PO, TO and EO are on their Ontology explorer


_______________________________________________________________________

AgBase- only has annotations to GO

ARTADE2DB- link not working?

Biolod.org example page: non-secretory trichome see also: plant structure - site and links not working?

Brassibase- No PO on their site

cosmoss- No PO on their site

Cyverse- mirror site of planteome, otherwise not sure how it is being used

G to L

Gramene Archive- Old ontology browsers, can browse PO, TO, PECO, and GO

Gramene Biomart- can filter by PO and GO

Grape genome database

Query page CRIBI- Grape genes are annotated to PO terms

_____________________________________________________________________________________________________________

Gene Ontology- No PO or TO?

Live Plant Image Group- has links to browse PO, but not sure how it is used

M to P

MAGIC- 'MAize Gene expressIon Compendium'- a web-based interface for exploring and analyzing a comprehensive maize-specific cross-platform expression compendium.

  • This compendium was constructed by collecting, homogenizing and formally annotating publicly available microarrays from Gene Expression Omnibus (GEO), and ArrayExpress. Includes plant ontology annotations

MaizeGDB Genes- PO annotations are listed on Gene pages from Sekhon study.

Maize cell Genomics database- images tagged with PO ids

Manually Curated Database of Rice Proteins- Data is tagged with PO, TO and PECO terms

Metabolomic Repository Bordeaux MeRy- plant metabolomics platform allowing the storage and visualisation of Nuclear Magnetic Resonance (NMR) metabolic profiles from plants, but has old version of PO and EO

The Compositae Genome Project (CGP)- Morphodb Cool PO browser with links to annotated data from lettuce and sunflower, really old version of PO

Oryzabase PO Version - Japanese version of old PO (plant structures only translated)

Phenopsis - from INRA, information system dedicated to the model plant Arabidopsis thaliana; ontology terms are out of date on here, links go go to the EBI OLS

POEAS- Plant Ontology Enrichment Analysis Server, automated Plant Phenomic Analysis Using Plant Ontology terms based on genes from Arabidopsis thaliana


Plant-specimen-contextual-data-consensus

_________________________________________________________________________________________________________

The Integrated Databases of Plant Omics Data- link not working

OntoBrowser- interactive ontology navigator and ontology-based image retrieval system. It makes use of an ontology to retrieve images. page not loading...

Plant Phenome- on Biolod, links not functional

NASC Ontology page- link to ontology browser is not functional

Oryzabase- no links to PO terms

Plantsystematics.org- ?? cant find any PO ref

PRIDE- PRoteomics IDEntifications (PRIDE) database, used to have a ontology query, but cannot find it now

R to Z

RARGEII- RIKEN Arabidopsis Genome Encyclopedia, Search mutant lines by phenotypes- use PO or PATO

Solanaceae Genome network (SGN)- can browse/search by GO,PO, SO, PATO

SuperFamily Phenotype Browser

  • Prefix changed to AP - 'Arabidopsis Plant ontology' with 2 subontologies (PAN for Plant ANatomical entity, PDE for Plant structure DEvelopment stage), "AP:0025099" used here is equivalent to "PO:0025099" in original ontology
  • need to address some issues here, not an "Arabidopsis Plant Ontology"

Virtual plant- browse the Plant Ontology to see Arabidopsis genes annotated to that term

TAIR - GO_and_PO_Annotations can be downloaded, browse by ontology terms

Wheat Data Interoperability Guidelines - Recommendations prepared by the Wheat Data Interoperability Working Group, of the Research Data Alliance

________________________________________________________________________________________________

SoyBase- AmiGO browser of Soy Ontology terms, not mapped to PO or TO- just to SOY ontology

Traitnet- no ontology searches etc from their site...

Uniprot keywords- can search for GO terms, no use of PO ??

Others?

not actually using the PO but should be:

Bio-Array Resource for Plant Biology (BAR)

Genevestigator

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