Latest revision as of 17:31, 5 September 2017

Ontology Listing Services, etc

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

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

Ref: Annotare—a tool for annotating high-throughput biomedical investigations and resulting data Bioinformatics, Volume 26, Issue 19, 1 October 2010, Pages 2470–2471

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

REF: MAGIC: access portal to a cross-platform gene expression compendium for maize- Fu et al (2014), Bioinformatics. doi: 10.1093/bioinformatics/btt739

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

see page: PO terms

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

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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

@@ Line 3: / Line 3: @@
 [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]
@@ Line 10: / Line 12: @@
 [http://ontofox.hegroup.org/ OntoFox]- web-based Ontology tool that fetches ontology terms and axioms
-[http://www.ontobee.org/ OntoBee]
+[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
+[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
@@ Line 23: / Line 27: @@
 [https://arapheno.1001genomes.org/ontology/PTO/ Arapheno] - search by TO or EO, weird versions
-[http://www.brenda-enzymes.info/ BRENDA]- mostly uses BTO, but old version of PO, TO and EO are on it
+[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
 _______________________________________________________________________
@@ Line 42: / Line 50: @@
 =G to L=
-[http://archive.gramene.org/plant_ontology/ Gramene Archive]- Old ontology browsers
+[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
@@ Line 49: / Line 57: @@
 [http://genomes.cribi.unipd.it/cgi-bin/pqs2/query.pl?release=v1#Ontologies Query page CRIBI]- Grape genes are annotated to PO terms
-[https://sites.google.com/site/liveplantimagegroup/home Live Plant Image Group]- has links to browse PO, but not sure how it is used
 _____________________________________________________________________________________________________________
 [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
@@ Line 66: / Line 76: @@
 [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]- tagged with TO terms
+[http://www.genomeindia.org/biocuration/ Manually Curated Database of Rice Proteins]- Data is tagged with PO, TO and PECO terms
 [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
-[http://compgenomics.ucdavis.edu/morphodb/analysis/viewOntology.php Morphodb]- Cool PO browser with links to annotated data from lettuce and sunflower, really old version of PO
+[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
-[https://shigen.nig.ac.jp/rice/oryzabase/ Oryzabase]-
+[http://shigen.nig.ac.jp/plantontology/ja/go Oryzabase PO Version ]- Japanese version of old PO (plant structures only translated)
-[http://shigen.nig.ac.jp/plantontology/ja/go Japanese version of PO (plant structures)]
 [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
@@ Line 80: / Line 88: @@
 [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
+[https://academic.oup.com/gigascience/article/5/1/1/2756883/Plant-specimen-contextual-data-consensus Plant-specimen-contextual-data-consensus]
 _________________________________________________________________________________________________________
@@ Line 89: / Line 100: @@
 [http://biolod.org/database/ria224i/Plant_Phenome Plant Phenome]- on Biolod, links not functional
-[http://arabidopsis.info/NASC Ontology page]- link to ontology browser is not functional
+[http://arabidopsis.info/NASC NASC Ontology page]- link to ontology browser is not functional
+[https://shigen.nig.ac.jp/rice/oryzabase/ Oryzabase]- no links to PO terms
 [http://www.plantsystematics.org Plantsystematics.org]- ?? cant find any PO ref
@@ Line 99: / Line 112: @@
 [http://rarge-v2.psc.riken.jp/ RARGEII]- RIKEN Arabidopsis Genome Encyclopedia, Search mutant lines by phenotypes- use PO or PATO
-[http://semantic-json.org/sw/wiki/en/cria160s1ria160s5i/#applications Riken]- link not working...
+[http://solgenomics.net/tools/onto/index.pl Solanaceae Genome network (SGN)]- can browse/search by GO,PO, SO, PATO
+[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://solgenomics.net/tools/onto/index.pl Solanaceae Genome network (SGN)]- can browse/search by GO,PO, SO, PATO
+[http://virtualplant.bio.nyu.edu/cgi-bin/vpweb/ Virtual plant]- browse the Plant Ontology to see Arabidopsis genes annotated to that term
+[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
-[https://soybase.org/ SoyBase]- AmiGO browser of Soy Ontology terms, not mapped to PO or TO
+________________________________________________________________________________________________
-[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://soybase.org/ SoyBase]- AmiGO browser of Soy Ontology terms, not mapped to PO or TO- just to SOY ontology
 [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 ??
-[http://virtualplant.bio.nyu.edu/cgi-bin/vpweb/ Virtual plant]- browse the Plant Ontology to see Arabidopsis genes annotated to that term
-[https://www.arabidopsis.org/ TAIR] - GO_and_PO_Annotations can be downloaded, browse by ontology terms
 =Others?=
@@ Line 119: / Line 136: @@
 [http://bar.utoronto.ca/welcome.htm Bio-Array Resource for Plant Biology (BAR)]
-[http://www.cropontology.org/ Crop Ontology]
 [https://www.genevestigator.com/gv/plant.jsp Genevestigator]

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

Latest revision as of 17:31, 5 September 2017

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Ontology Listing Services, etc

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M to P

R to Z

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