Difference between revisions of "Links to sites using the PO"
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[http://bioportal.bioontology.org/ Bioportal] | [http://bioportal.bioontology.org/ Bioportal] | ||
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| + | [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.ebi.ac.uk/ontology-lookup/browse.do?ontName=PO EBI OLS] | ||
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[http://ontofox.hegroup.org/ OntoFox]- web-based Ontology tool that fetches ontology terms and axioms | [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://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 | [http://www.metabolomics-msi.org/ Metabolomics Standards Initiative]- PO is recommended in MSI standards | ||
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| + | [https://www.agbiodata.org/ AgBioData Site]- Consortium of agricultural biological databases and associated resources | ||
=A to F= | =A to F= | ||
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[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]) | [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]- mostly uses BTO, but old version of PO, TO and EO are on | + | [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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=G to L= | =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 | [http://ensembl.gramene.org/biomart/martview/a5af63c60de7ebc805c5f558d7459deb Gramene Biomart]- can filter by PO and GO | ||
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[http://genomes.cribi.unipd.it/cgi-bin/pqs2/query.pl?release=v1#Ontologies Query page CRIBI]- Grape genes are annotated to PO terms | [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? | [http://www.geneontology.org/ Gene Ontology]- No PO or TO? | ||
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| + | [https://sites.google.com/site/liveplantimagegroup/home Live Plant Image Group]- has links to browse PO, but not sure how it is used | ||
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[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. | [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. | ||
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* This compendium was constructed by collecting, homogenizing and formally annotating publicly available microarrays from Gene Expression Omnibus (GEO), and ArrayExpress. Includes plant ontology annotations | * This compendium was constructed by collecting, homogenizing and formally annotating publicly available microarrays from Gene Expression Omnibus (GEO), and ArrayExpress. Includes plant ontology annotations | ||
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* 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 | * 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 | ||
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[http://maize.jcvi.org/cellgenomics/ecell.php?search=10 Maize cell Genomics database]- images tagged with PO ids | [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://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 | + | [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 |
[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 Oryzabase PO Version ]- Japanese version of old PO (plant structures only translated) | ||
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[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 | [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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| + | [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://bar.utoronto.ca/welcome.htm Bio-Array Resource for Plant Biology (BAR)] | [http://bar.utoronto.ca/welcome.htm Bio-Array Resource for Plant Biology (BAR)] | ||
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[https://www.genevestigator.com/gv/plant.jsp Genevestigator] | [https://www.genevestigator.com/gv/plant.jsp Genevestigator] | ||
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
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
_________________________________________________________________________________________________________
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
- 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
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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:
