The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.


:The Plant Ontology Consortium (POC, is a collaborative effort among model plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a controlled vocabulary (ontology) for plants. The ontology allows users to ascribe attributes of plant structure (anatomy and morphology) and developmental stages to data types, such as genes and phenotypes, to provide a semantic framework to make meaningful cross-species and database comparisons. The POC builds upon groundbreaking work by the Gene Ontology Consortium (GOC) by adopting and extending the GOC's principles, existing software and database structure. Over the past year, POC has added hundreds of ontology terms to associate with thousands of genes and gene products from Arabidopsis, rice and maize, which are available through a newly updated web-based browser ( for viewing, searching and querying. The Consortium has also implemented new functionalities to facilitate the application of PO in genomic research and updated the website to keep the contents current. In this report, we present a brief description of resources available from the website, changes to the interfaces, data updates, community activities and future enhancement.


Nucleic Acids Res


Nucleic acids research


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




Has Abstract


2008-01-01 00:00:00




Database issue










  • MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca.

    abstract::Mollusca represents the second largest animal phylum but remains poorly explored from a genomic perspective. While the recent increase in genomic resources holds great promise for a deep understanding of molluscan biology and evolution, access and utilization of these resources still pose a challenge. Here, we present...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Liu F,Li Y,Yu H,Zhang L,Hu J,Bao Z,Wang S

    更新日期:2021-01-08 00:00:00

  • The mechanism of mutation induction by a hydrogen bond ambivalent, bicyclic N4-oxy-2'-deoxycytidine in Escherichia coli.

    abstract::The triphosphate of the nucleoside deoxyribosyl dihydropyrimido[4,5-c][1,2]oxazin-7-one (dP) is known to be incorporated into DNA efficiently by Taq polymerase and is a useful tool for polymerase-mediated in vitro mutagenesis. It is shown here that dP is a potent mutagen in Escherichia coli and Salmonella typhimurium ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Negishi K,Williams DM,Inoue Y,Moriyama K,Brown DM,Hayatsu H

    更新日期:1997-04-15 00:00:00

  • Characterization of clinically used oral antiseptics as quadruplex-binding ligands.

    abstract::Approaches to characterize the nucleic acid-binding properties of drugs and druglike small molecules are crucial to understanding the behavior of these compounds in cellular systems. Here, we use a Small Molecule Microarray (SMM) profiling approach to identify the preferential interaction between chlorhexidine, a wide...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Calabrese DR,Zlotkowski K,Alden S,Hewitt WM,Connelly CM,Wilson RM,Gaikwad S,Chen L,Guha R,Thomas CJ,Mock BA,Schneekloth JS Jr

    更新日期:2018-04-06 00:00:00

  • Processing of complementary sense RNAs of Digitaria streak virus in its host and in transgenic tobacco.

    abstract::We have used a polymerase chain reaction (PCR) procedure to analyse low abundance complementary sense RNAs of Digitaria streak virus (DSV) from infected leaves of Digitaria setigera. This study has confirmed that both spliced and unspliced RNAs are synthesised by the same transcription unit. The position of the intron...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mullineaux PM,Guerineau F,Accotto GP

    更新日期:1990-12-25 00:00:00

  • Systematic use of synthetic 5'-UTR RNA structures to tune protein translation improves yield and quality of complex proteins in mammalian cell factories.

    abstract::Predictably regulating protein expression levels to improve recombinant protein production has become an important tool, but is still rarely applied to engineer mammalian cells. We therefore sought to set-up an easy-to-implement toolbox to facilitate fast and reliable regulation of protein expression in mammalian cell...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Eisenhut P,Mebrahtu A,Moradi Barzadd M,Thalén N,Klanert G,Weinguny M,Sandegren A,Su C,Hatton D,Borth N,Rockberg J

    更新日期:2020-11-18 00:00:00

  • Unique sequences are interspersed among tandemly repeated elements in the murine gamma 1 switch segment.

    abstract::Early in its differentiative pathway, a given B lymphocyte expresses immunoglobulin of the mu heavy chain class (IgM). Subsequent differentiative processes may involve rearrangement within the immunoglobulin heavy chain chromosomal locus to enable cells of the same lineage to synthesize immunoglobulins of other heavy ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mowatt M,Dery C,Dunnick W

    更新日期:1985-01-11 00:00:00

  • Computational detection and suppression of sequence-specific off-target phenotypes from whole genome RNAi screens.

    abstract::A challenge for large-scale siRNA loss-of-function studies is the biological pleiotropy resulting from multiple modes of action of siRNA reagents. A major confounding feature of these reagents is the microRNA-like translational quelling resulting from short regions of oligonucleotide complementarity to many different ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhong R,Kim J,Kim HS,Kim M,Lum L,Levine B,Xiao G,White MA,Xie Y

    更新日期:2014-07-01 00:00:00

  • RNApredator: fast accessibility-based prediction of sRNA targets.

    abstract::Bacterial genomes encode a plethora of small RNAs (sRNAs), which are heterogeneous in size, structure and function. Most sRNAs act as post-transcriptional regulators by means of specific base pairing interactions with the 5'-untranslated region of mRNA transcripts, thereby modifying the stability of the target transcr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Eggenhofer F,Tafer H,Stadler PF,Hofacker IL

    更新日期:2011-07-01 00:00:00

  • Thermodynamic comparison of PNA/DNA and DNA/DNA hybridization reactions at ambient temperature.

    abstract::The thermodynamics of 13 hybridization reactions between 10 base DNA sequences of design 5'-ATGCXYATGC-3' with X, Y = A, C, G, T and their complementary PNA and DNA sequences were determined from isothermal titration calorimetry (ITC) measurements at ambient temperature. For the PNA/DNA hybridization reactions, the bi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Schwarz FP,Robinson S,Butler JM

    更新日期:1999-12-15 00:00:00

  • T1DBase: update 2011, organization and presentation of large-scale data sets for type 1 diabetes research.

    abstract::T1DBase ( is web platform, which supports the type 1 diabetes (T1D) community. It integrates genetic, genomic and expression data relevant to T1D research across mouse, rat and human and presents this to the user as a set of web pages and tools. This update describes the incorporation of new dat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Burren OS,Adlem EC,Achuthan P,Christensen M,Coulson RM,Todd JA

    更新日期:2011-01-01 00:00:00

  • Regulation of gene amplification and expression in cells that constitutively express a temperature sensitive SV40 T-antigen.

    abstract::Simian cells have been transformed with SV40 origin-defective recombinant plasmids containing the tsA209 T-antigen gene. These plasmids contain deletions of either 5 or 52 nucleotides that include the BglI site at the SV40 ori, are defective for replication in COS-1 cells but retain a functional SV40 early promoter. T...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Portela A,de la Luna S,Melero JA,Vara J,Jiménez A,Ortín J

    更新日期:1985-11-25 00:00:00

  • Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization.

    abstract::Vascular endothelial growth factor A (VEGF-A) is a master regulator of angiogenesis, vascular development and function. In this study we investigated the transcriptional regulation of VEGF-A-responsive genes in primary human aortic endothelial cells (HAECs) and human umbilical vein endothelial cells (HUVECs) using gen...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kaikkonen MU,Niskanen H,Romanoski CE,Kansanen E,Kivelä AM,Laitalainen J,Heinz S,Benner C,Glass CK,Ylä-Herttuala S

    更新日期:2014-11-10 00:00:00

  • PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes.

    abstract::The PRISM web server enables fast and accurate prediction of protein-protein interactions (PPIs). The prediction algorithm is knowledge-based. It combines structural similarity and accounts for evolutionary conservation in the template interfaces. The predicted models are stored in its repository. Given two protein st...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Baspinar A,Cukuroglu E,Nussinov R,Keskin O,Gursoy A

    更新日期:2014-07-01 00:00:00

  • Synthesis and hybridization studies of oligonucleotides containing 1-(2-deoxy-2-alpha-C-hydroxymethyl-beta-D-ribofuranosyl)thymine (2'-alpha-hm-dT).

    abstract::We report the first investigation of oligoribonucleotides containing a few 1-(2-deoxy-2-alpha-C-hydroxymethyl-beta-D-ribofuranosyl)thymine units (or 2'-hm-dT, abbreviated in this work as 'H'). Both the 2'-CH2O-phosphoramidite and 3'-O-phosphoramidite derivatives of H were synthesized and incorporated into both 2',5'-R...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Peng CG,Damha MJ

    更新日期:2005-12-23 00:00:00

  • Terminal labeling and addition of homopolymer tracts to duplex DNA fragments by terminal deoxynucleotidyl transferase.

    abstract::Terminal deoxynucleotidyl transferase, which requires a single-stranded DNA primer under the usual assay conditions, can be made to accept double-stranded DNA as primer for the addition of either rNMP or dNMP, if Mg+2 ion is replaced by Co+2 ion. The priming efficiency in the presence of (C leads to) CO+2 ion with res...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Roychoudhury R,Jay E,Wu R

    更新日期:1976-01-01 00:00:00

  • Determination of the molecular weight of DNA-bound protein(s) responsible for gel electrophoretic mobility shift of linear DNA fragments examplified with purified viral myb protein.

    abstract::A protein-DNA complex has less gel electrophoretic mobility than the free DNA fragment. One parameter for the degree of retardation of a linear DNA fragment in a protein-DNA complex is the molecular weight of the bound protein(s). The quotient of the migration distances of free DNA (m) and protein-DNA complex (m') is ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bading H

    更新日期:1988-06-24 00:00:00

  • Association between translation efficiency and horizontal gene transfer within microbial communities.

    abstract::Horizontal gene transfer (HGT) is a major force in microbial evolution. Previous studies have suggested that a variety of factors, including restricted recombination and toxicity of foreign gene products, may act as barriers to the successful integration of horizontally transferred genes. This study identifies an addi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Tuller T,Girshovich Y,Sella Y,Kreimer A,Freilich S,Kupiec M,Gophna U,Ruppin E

    更新日期:2011-06-01 00:00:00

  • A novel CRISPR-engineered prostate cancer cell line defines the AR-V transcriptome and identifies PARP inhibitor sensitivities.

    abstract::Resistance to androgen receptor (AR)-targeted therapies in prostate cancer (PC) is a major clinical problem. A key mechanism of treatment resistance in advanced PC is the generation of alternatively spliced forms of the AR termed AR variants (AR-Vs) that are refractory to targeted agents and drive tumour progression. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kounatidou E,Nakjang S,McCracken SRC,Dehm SM,Robson CN,Jones D,Gaughan L

    更新日期:2019-06-20 00:00:00

  • Post-mitotic BET-induced reshaping of integrase quaternary structure supports wild-type MLV integration.

    abstract::The Moloney murine leukemia virus (MLV) is a prototype gammaretrovirus requiring nuclear disassembly before DNA integration. In the nucleus, integration site selection towards promoter/enhancer elements is mediated by the host factor bromo- and extraterminal domain (BET) proteins (bromodomain (Brd) proteins 2, 3 and 4...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Borrenberghs D,Zurnic I,De Wit F,Acke A,Dirix L,Cereseto A,Debyser Z,Hendrix J

    更新日期:2019-02-20 00:00:00

  • Tissue-dependent isoforms of mammalian Fox-1 homologs are associated with tissue-specific splicing activities.

    abstract::An intronic hexanucleotide UGCAUG has been shown to play a critical role in the regulation of tissue-specific alternative splicing of pre-mRNAs in a wide range of tissues. Vertebrate Fox-1 has been shown to bind to this element, in a highly sequence-specific manner, through its RNA recognition motif (RRM). In mammals,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Nakahata S,Kawamoto S

    更新日期:2005-04-11 00:00:00

  • Synthesis and characterization of a ribavirin-3',5'-phosphate pentadecamer homoribopolymer bearing a 5'-amino tether group and a 3'-thymidine.

    abstract::The synthesis of a pentadecamer of the 5'-phosphate of the antiviral nucleoside ribavirin (1'-beta-D-ribofuranosyl-1H-1,2,4-triazole-3-carboxamide) has been achieved. This homoribopolymer is terminated at the 5'-position with an (6-aminohexyl)phosphate group to permit conjugation to a carrier and at the 3'-position by...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Dawson MI,Jina AN,Torkelson S,Rhee S,Moore M,Zarling DA,Hobbs PD

    更新日期:1990-03-11 00:00:00

  • Transcription initiation sites within an IS2 insertion in a Gal-constitutive mutant of Escherichia coli.

    abstract::Insertion of the insertion sequence Is2(I) directly before the galE gene of the galactose operon results in a Gal minus phenotype (1, 2). The Gal-constitutive allele galc200 (and its deletion derivative galc200 delta 31) arise from such a Gal minus mutant by the insertion of LS2(II) DNA within the LS2(I) sequence (3)....

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hinton DM,Musso RE

    更新日期:1982-08-25 00:00:00

  • A systemic transcriptome analysis reveals the regulation of neural stem cell maintenance by an E2F1-miRNA feedback loop.

    abstract::Stem cell fate decisions are controlled by a molecular network in which transcription factors and miRNAs are of key importance. To systemically investigate their impact on neural stem cell (NSC) maintenance and neuronal commitment, we performed a high-throughput mRNA and miRNA profiling and isolated functional interac...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Palm T,Hemmer K,Winter J,Fricke IB,Tarbashevich K,Sadeghi Shakib F,Rudolph IM,Hillje AL,De Luca P,Bahnassawy L,Madel R,Viel T,De Siervi A,Jacobs AH,Diederichs S,Schwamborn JC

    更新日期:2013-04-01 00:00:00

  • WikiPathways: building research communities on biological pathways.

    abstract::Here, we describe the development of WikiPathways (, a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kelder T,van Iersel MP,Hanspers K,Kutmon M,Conklin BR,Evelo CT,Pico AR

    更新日期:2012-01-01 00:00:00

  • The Reactome pathway knowledgebase.

    abstract::Reactome ( is a manually curated open-source open-data resource of human pathways and reactions. The current version 46 describes 7088 human proteins (34% of the predicted human proteome), participating in 6744 reactions based on data extracted from 15 107 research publications with PubMed link...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Croft D,Mundo AF,Haw R,Milacic M,Weiser J,Wu G,Caudy M,Garapati P,Gillespie M,Kamdar MR,Jassal B,Jupe S,Matthews L,May B,Palatnik S,Rothfels K,Shamovsky V,Song H,Williams M,Birney E,Hermjakob H,Stein L,D'Eusta

    更新日期:2014-01-01 00:00:00

  • Intracellular RNA cleavage by the hairpin ribozyme.

    abstract::Studies involving ribozyme-directed inactivation of targeted RNA molecules have met with mixed success, making clear the importance of methods to measure and optimize ribozyme activity within cells. The interpretation of biochemical assays for determining ribozyme activity in the cellular environment have been complic...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Seyhan AA,Amaral J,Burke JM

    更新日期:1998-08-01 00:00:00

  • Capping of vesicular stomatitis virus pre-mRNA is required for accurate selection of transcription stop-start sites and virus propagation.

    abstract::The multifunctional RNA-dependent RNA polymerase L protein of vesicular stomatitis virus catalyzes unconventional pre-mRNA capping via the covalent enzyme-pRNA intermediate formation, which requires the histidine-arginine (HR) motif in the polyribonucleotidyltransferase domain. Here, the effects of cap-defective mutat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ogino T

    更新日期:2014-10-29 00:00:00

  • Comparative analysis of chimeric ZFP-, TALE- and Cas9-piggyBac transposases for integration into a single locus in human cells.

    abstract::Integrating DNA delivery systems hold promise for many applications including treatment of diseases; however, targeted integration is needed for improved safety. The piggyBac (PB) transposon system is a highly active non-viral gene delivery system capable of integrating defined DNA segments into host chromosomes witho...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Luo W,Galvan DL,Woodard LE,Dorset D,Levy S,Wilson MH

    更新日期:2017-08-21 00:00:00

  • Glycosyl conformational and inductive effects on the acid catalysed hydrolysis of purine nucleosides.

    abstract::The log kobs vs. pH profiles were determined in the intermediate acidity region for the glycosyl hydrolysis of guanosine and its 8-amino, 8-monomethylamino, 8-dimethylamino and 8-bromo derivatives. The decreased rate of the 8-amino and enhanced rate of the 8-bromo compound compared to guanosine support an A type mecha...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Jordan F,Niv H

    更新日期:1977-03-01 00:00:00

  • The C/ebp-Atf response element (CARE) location reveals two distinct Atf4-dependent, elongation-mediated mechanisms for transcriptional induction of aminoacyl-tRNA synthetase genes in response to amino acid limitation.

    abstract::The response to amino acid (AA) limitation of the entire aminoacyl-tRNA synthetase (ARS) gene family revealed that 16/20 of the genes encoding cytoplasmic-localized enzymes are transcriptionally induced by activating transcription factor 4 (Atf4) via C/ebp-Atf-Response-Element (CARE) enhancers. In contrast, only 4/19 ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Shan J,Zhang F,Sharkey J,Tang TA,Örd T,Kilberg MS

    更新日期:2016-11-16 00:00:00