scholarly journals The Rice Annotation Project Database (RAP-DB): 2008 update

2007 ◽  
Vol 36 (Database) ◽  
pp. D1028-D1033 ◽  
Author(s):  
Keyword(s):  
Annotation Project ◽  
Rice Annotation Project

scholarly journals Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics

2013 ◽  
Vol 54 (2) ◽  
pp. e6-e6 ◽  
Author(s):  
Hiroaki Sakai ◽  
Sung Shin Lee ◽  
Tsuyoshi Tanaka ◽  
Hisataka Numa ◽  
Jungsok Kim ◽  
...  
Keyword(s):  
Annotation Project ◽  
Rice Annotation Project

scholarly journals Lexicons, Literacies and Design Futures

2020 ◽  
pp. 114-149
Author(s):  
Andrew Morrison ◽  
Nina Bjørnstad ◽  
Einar Sneve Martinussen ◽  
Bjørn Johansen ◽  
Bastien Kerspern ◽  
...  
Keyword(s):  
Resource Use ◽  
Design Education ◽  
Narrative Fiction ◽  
Work Package ◽  
3 Dimensional ◽  
The Public ◽  
Multimodal Discourse ◽  
Cultural Life ◽  
Annotation Project ◽  
Design Council

As the world in which we live becomes more complex and contested, economically and politically but also in terms of rapid and long-lasting environmental change, design education faces new demands and challenges. We frame and situate these in terms of what we call “design futures literacies.” At stake in such a framing is a rethinking of design’s priorities in the context of climate change and resource use and reuse in futures that are uncertain, contingent and emergent. The article positions design as having shifted away from a techno-modernist design solutionism and to how it may engage in shaping futures through experimentation and exploration in the critical and productive engagement with techno-cultural life. These arguments are located within the prior experience of the transdisciplinary team of co-authors as well as a European level project between four leading design universities. The article takes up their first work package on the co-creation of a Lexicon for Design Futures Literacies and early experimentation towards generating resources and experience for its wider use. The article addresses the largely under articulated relations between language and design (from lexis to discourse). First, we present the development of an alphabetic, lexical semantic set and core grouping of design and futures terms. This vocabulary, drawn from a range of sources and experiences, is linked to the design of a related lexically centred card game. Second, the focus on vocabulary was extended to a section on situating lexis in cultural historical contexts, 3-dimensional haptic form giving and the language of abstraction. This was achieved via reference to a design narrative fiction experiment on emerging technologies and a historical costume annotation project as a prompt for making connections between items from the lexicon and modelling abstract forms in clay. Third, in collaboration with a government ministry and a design council, students developed four future digital urban living scenarios with trust as their central focus. “Languaging” the future was embodied in physical scenarios open to the public, connected to a professional seminar and to international research events where verbal descriptions, explanations and reflections were voiced by the students alongside their educator-researcher. The article closes with suggestions that there is further opportunity for attention to lexis and multimodal discourse modes in shaping design futures literacies, within and across the project but also in practice, in policy and for and as design pedagogy.

scholarly journals In silico analysis of transcription factor binding sites in promoters of germin-like protein genes in rice

2016 ◽  
Vol 68 (4) ◽  
pp. 863-876 ◽  
Author(s):  
Muhammad Ilyas ◽  
Syed Naqvi ◽  
Tariq Mahmood
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
In Silico ◽  
In Silico Analysis ◽  
Chromosome 8 ◽  
Upstream Region ◽  
Asian Rice ◽  
Homeobox Protein ◽  
Annotation Project ◽  
Tata Box Binding Protein

Germins (GERs) and germin-like proteins (GLPs) play important roles in responses to various stresses; however, their function is still not fully understood. Significant insight into their function can be obtained by analyzing their promoters. In the present study, the 5' upstream promoters (1000 bp) of 43 Asian rice (Oryza sativa var. Japonica) GLP genes were retrieved from the Plant Ensemble, based on the Rice Annotation Project database (RAP-DB). Phylogenetic analysis via MEGA6 showed a narrow genetic background (0.2%) with a Tajima neutrality value (?) of 0.69. Overall, 4234 transcription factor (TF) binding sites (TFBSs) were found on chromosomes 1, 2, 3, 4, 5, 8, 9, 11 and 12 via ?MatInspector? from 90 different TF families using a total of 444 families. Common TFs and DiAlign analyses showed that arabidopsis homeobox protein (AHBP), MYB-like proteins (MYBL) and vertebrate TATA-box-binding protein (VTBP) were the most abundant, common and evolutionarily conserved elements in the upstream region from 0 to -800. Finding their mutual interaction via Farmworker analysis uncovered three new cisregulatory modules (VTBP_VTBP, MYBS_MYBS, and AHBP_VTBP), which appear to be decisive for OsGLP regulation. In silico functional analysis via ModelInspector revealed 77 cis-regulatory modules, each comprised of two elements, among which DOFF_OPAQ_03 and GTBX_MYCL_01 were the most frequent and mostly found on chromosome 8 and 12, indicating that the combinatorial interaction of these elements has a fundamental role in various biological processes. The study revealed the importance of these elements in regulating OsGLP expression that will help in predicting the role of these genes in various stresses, and can have application in biotechnology.

TBCAP; tuberculosis annotation project

Tuberculosis ◽  
2013 ◽  
Vol 93 (1) ◽  
pp. 1-5 ◽  
Author(s):  
Patrick J. Brennan ◽  
Roland Brosch ◽  
Bruce Birren ◽  
Bruno Sobral
Keyword(s):  
Annotation Project

An XML engine to model and query multimodal concurrent linguistic annotations

2011 ◽  
Author(s):  
Julien Seinturier ◽  
Elisabeth Murisasco ◽  
Emmanuel Bruno
Keyword(s):  
Information System ◽  
Social Science ◽  
Computer Science ◽  
Linguistic Knowledge ◽  
Temporal Relations ◽  
Speech Corpus ◽  
Annotation Project ◽  
Unique Framework

This paper presents an XML engine defined to model and query multimodal concurrent annotated data. This work stands in the context of the OTIM (Tools for Multimodal Annotation) project which aims at developing conventions and tools for multimodal annotation of a large conversational French speech corpus; it groups together Social Science and Computer Science researchers. Within OTIM, our objective is to provide linguists with a unique framework to encode and manipulate numerous linguistic domains: morpho-syntax, prosody, phonetics, disfluencies, discourse, gesture and posture. For that, it has to be possible to bring together and align all the different pieces of information (called annotations) associated to a corpus. We propose a complete pipeline from the annotation step to the management of the data within an XML Information System. This pipeline first relies on the formalisation of the linguistic knowledge and data within a OTIM specific XML format. A Java framework is proposed for interfacing with both linguists specific annotation tools and XML Information System. Finally, the querying of multimodal annotations within the XML information system using XQuery is presented. As annotations are time aligned, an extension of XQuery to Allen temporal relations is proposed. The paper conclude on a discussion about the interest of a pure XML approach for linguistic annotations information system and the question of the integration of the semantic within the pipeline.

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