Planteome
Homepage http://www.planteome.org
Countries that developed this resource United States
Created in 2013
Taxonomic range
Knowledge Domains
Subjects
User-defined Tags
How to cite this record FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jun 01 2020 4:36 p.m.
Record added: Nov. 1, 2017, 10:54 p.m.
Record updated:
Sept. 18, 2018, 2:32 p.m. by The FAIRsharing Team.
| contact form | Feedback and Contact |
| online documentation | Access Ontology and Software files |
Additional Information
| Contact | Pankaj Jaiswal ORCID |
| Ontology Enrichment Analysis Tool | http://planteome.org/oat/ | 1.0 Beta |
| Planteome Noctua (community gene annotation tool) | http://noctua.planteome.org/ | 1.0 Beta |
Conditions of Use
Applies to: Data use Applies to: Database softwareData Access
| Bioentity Search | http://browser.planteome.org/amigo/search/bioentity |
The Plant Ontology: A Tool for Plant Genomics.
Cooper L,Jaiswal P
Methods Mol Biol 2015
An ontology approach to comparative phenomics in plants.
Oellrich A,Walls RL,Cannon EK,Cannon SB,Cooper L,Gardiner J,Gkoutos GV,Harper L,He M,Hoehndorf R,Jaiswal P,Kalberer SR,Lloyd JP,Meinke D,Menda N,Moore L,Nelson RT,Pujar A,Lawrence CJ,Huala E
Plant Methods 2015
AISO: Annotation of Image Segments with Ontologies.
Lingutla NT,Preece J,Todorovic S,Cooper L,Moore L,Jaiswal P
J Biomed Semantics 2015
Finding our way through phenotypes.
Deans AR,Lewis SE,Huala E,Anzaldo SS,Ashburner M,Balhoff JP,Blackburn DC,Blake JA,Burleigh JG,Chanet B,Cooper LD,Courtot M,Csosz S,Cui H,Dahdul W,Das S,Dececchi TA,Dettai A,Diogo R,Druzinsky RE,Dumontier M,Franz NM,Friedrich F,Gkoutos GV,Haendel M,Harmon LJ,Hayamizu TF,He Y,Hines HM,Ibrahim N,Jackson LM,Jaiswal P,James-Zorn C,Kohler S,Lecointre G,Lapp H,Lawrence CJ,Le Novere N,Lundberg JG,Macklin J,Mast AR,Midford PE,Miko I,Mungall CJ,Oellrich A,Osumi-Sutherland D,Parkinson H,Ramirez MJ,Richter S,Robinson PN,Ruttenberg A,Schulz KS,Segerdell E,Seltmann KC,Sharkey MJ,Smith AD,Smith B,Specht CD,Squires RB,Thacker RW,Thessen A,Fernandez-Triana J,Vihinen M,Vize PD,Vogt L,Wall CE,Walls RL,Westerfeld M,Wharton RA,Wirkner CS,Woolley JB,Yoder MJ,Zorn AM,Mabee P
PLoS Biol 2015
The plant ontology as a tool for comparative plant anatomy and genomic analyses.
Cooper L,Walls RL,Elser J,Gandolfo MA,Stevenson DW,Smith B,Preece J,Athreya B,Mungall CJ,Rensing S,Hiss M,Lang D,Reski R,Berardini TZ,Li D,Huala E,Schaeffer M,Menda N,Arnaud E,Shrestha R,Yamazaki Y,Jaiswal P
Plant Cell Physiol 2012
Ontologies as integrative tools for plant science.
Walls RL,Athreya B,Cooper L,Elser J,Gandolfo MA,Jaiswal P,Mungall CJ,Preece J,Rensing S,Smith B,Stevenson DW
Am J Bot 2012
Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages.
Jaiswal P,Avraham S,Ilic K,Kellogg EA,McCouch S,Pujar A,Reiser L,Rhee SY,Sachs MM,Schaeffer M,Stein L,Stevens P,Vincent L,Ware D,Zapata F
Comp Funct Genomics 2008
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.
Avraham S,Tung CW,Ilic K,Jaiswal P,Kellogg EA,McCouch S,Pujar A,Reiser L,Rhee SY,Sachs MM,Schaeffer M,Stein L,Stevens P,Vincent L,Zapata F,Ware D
Nucleic Acids Res 2008
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant.
Ilic K,Kellogg EA,Jaiswal P,Zapata F,Stevens PF,Vincent LP,Avraham S,Reiser L,Pujar A,Sachs MM,Whitman NT,McCouch SR,Schaeffer ML,Ware DH,Stein LD,Rhee SY
Plant Physiol 2006
Whole-plant growth stage ontology for angiosperms and its application in plant biology.
Pujar A,Jaiswal P,Kellogg EA,Ilic K,Vincent L,Avraham S,Stevens P,Zapata F,Reiser L,Rhee SY,Sachs MM,Schaeffer M,Stein L,Ware D,McCouch S
Plant Physiol 2006
Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase.
Yamazaki Y,Jaiswal P
Plant Cell Physiol 2005
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.
Cooper L,Meier A,Laporte MA,Elser JL,Mungall C,Sinn BT,Cavaliere D,Carbon S,Dunn NA,Smith B,Qu B,Preece J,Zhang E,Todorovic S,Gkoutos G,Doonan JH,Stevenson DW,Arnaud E,Jaiswal P
Nucleic Acids Res 2017
Reporting Guidelines
No guidelines defined
Terminology Artifacts
- Chemical Entities of Biological Interest
- Plant Environmental Ontology
- Evidence codes
- Plant Trait Ontology
- OBO ReLationship
- NCBI Taxonomy
- Phenotypic QualiTy Ontology
- Gene Ontology
- IBP Rice Trait Ontology
- Sweet Potato Ontology
- Crop Ontology
- IBP Crop Research Ontology
- OBO Relations Ontology
- Maize Ontology
- Plant Ontology
- IBP Wheat Plant Anatomy and Development Ontology
- Lentil Ontology
- Soybean Ontology
- IBP Cassava Trait Ontology
- Pigeon Pea Ontology
- Banana Ontology
- Chickpea Ontology
- Sorghum Ontology
- Groundnut Ontology
- IBP Cowpea Trait Ontology
- Plant Experimental Condition Ontology
Models and Formats
Identifier Schemas
No identifier schema standards defined
Metrics
No metrics standards defined
- The Arabidopsis Information Resource
- Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants
- Sol Genomics Network
- SoyBase
- Maize Genetics and Genomics Database
- Oryzabase
- Germplasm Resources Information Network
- Ontobee
- Ensembl Plants
- MusaBase
- SweetPotatoBase
- YamBase
- Cassavabase
This record is not implemented by any policy.
Record Maintainer
Funds
National Science Foundation (NSF), USA (Government body)
Maintains
Bioversity International, Rome, Italy (Consortium)
New York Botanical Garden (Research institute)
Oregon State University, USA (University)
Grant Number(s)
1340112 (National Science Foundation (NSF), USA)
