Difference between revisions of "Links to sites using the 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]- link to ontology browser is not functional | [http://arabidopsis.info/cgi-bin/ontology/nasc_po/go.cgi?search_constraint=terms&action=replace_tree&session_id=8730b1287179734 NASC Ontology page]- link to ontology browser is not functional | ||
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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 | ||
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[https://database.riken.jp/sw/en/Home/cria301u1i/ The Integrated Databases of Plant Omics Data]- link not working | [https://database.riken.jp/sw/en/Home/cria301u1i/ The Integrated Databases of Plant Omics Data]- link not working | ||
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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... | ||
[http://biolod.org/database/ria224i/Plant_Phenome Plant Phenome]- on Biolod, links not functional | [http://biolod.org/database/ria224i/Plant_Phenome Plant Phenome]- on Biolod, links not functional | ||
Revision as of 22:01, 29 August 2017
Ontology Listing Services
A to F
Annotare- Array Express experiment submission tool
- Ref: Annotare—a tool for annotating high-throughput biomedical investigations and resulting data Bioinformatics, Volume 26, Issue 19, 1 October 2010, Pages 2470–2471
0Arapheno - search by TO or EO, weird versions
BRENDA- mostly uses BTO, but old version of PO, TO and EO are on it
Compositae Genomics Project: Morphdb
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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 Biomart- can filter by PO and GO
Query page CRIBI- Grape genes are annotated to PO terms
Live Plant Image Group- has links to browse PO, but not sure how it is used
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Gene Ontology- No PO or TO?
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- 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- tagged with TO 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
Metabolomics Standards Initiative- PO is recommended in MSI standards
NASC Ontology page- link to ontology browser is not functional
OntoFox- web-based Ontology tool that fetches ontology terms and axioms
Plantsystematics.org- ?? cant find any PO ref
Phenopsis - information system dedicated to the model plant Arabidopsis thaliana; ontology terms are out of date on here, go to the EBI OLS,
POEAS - POEAS: Automated Plant Phenomic Analysis Using Plant Ontology
PRIDE- In query, there are a list of parameter types to choose from. If you pick PO, you get a list of terms.
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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
R to Z
RARGEII- RIKEN Arabidopsis Genome Encyclopedia, Search mutant lines by phenotypes- use PO or PATO
Riken- link not working...
Solanaceae Genome network (SGN)- can browse/search by GO,PO, SO, PATO
SoyBase- AmiGO browser of Soy Ontology terms, not mapped to PO or TO
SuperFamily - need to address some issues here, not an "Arabidopsis Plant Ontology".
Traitnet- no ontology searches etc from their site...
Uniprot keywords- can search for GO terms, no use of PO ??
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
Others?
not actually using the PO but should be:
