Manually Curated Database of Rice Proteins
Names
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Manually Curated Database of Rice Proteins
metasource: Fairsharing.org
version: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
MCDRP
metasource: Fairsharing.org
version: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Names
More detailed information about this field from each metasource.
Manually Curated Database of Rice Proteins
metasource: Fairsharing.orgversion: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
MCDRP
metasource: Fairsharing.orgversion: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Names
More detailed information about this field from each metasource.
Manually Curated Database of Rice Proteins
metasource: Fairsharing.orgversion: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
MCDRP
metasource: Fairsharing.orgversion: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
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The Manually Curated Database of Rice Proteins (MCDRP) is a manually-curated database based on published experimental data. The database contains data for rice proteins curated from experiments drawn from research articles. The database stores information including gene name, plant type, tissue and developmental stage. The homepage for this resource could not be loaded. Please contact us if you have any information regarding the current status of this resource.
Description
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The Manually Curated Database of Rice Proteins (MCDRP) is a manually-curated database based on published experimental data. The database contains data for rice proteins curated from experiments drawn from research articles. The database stores information including gene name, plant type, tissue and developmental stage. The homepage for this resource could not be loaded. Please contact us if you have any information regarding the current status of this resource.
metasource: Fairsharing.orgversion: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Manually Curated Database of Rice Proteins (MCDRP) is a unique manually curated database based on published experimental data. Semantic integration of scientific data is essential to gain a higher level of understanding of biological systems. Since the majority of scientific data is available as published literature, text mining is an essential step before the data can be integrated and made available for computer-based search in various databases. However, text mining is a tedious exercise and thus, there is a large gap in the data available in curated databases and published literature. Moreover, data in an experiment can be perceived from several perspectives, which may not reflect in the text based curation. In order to address such issues, we have demonstrated the feasibility of digitizing the experimental data itself by creating a database on rice proteins based on in-house developed data curation models. Digitization of experimental data itself offers several advantages: 1. Digitization renders the experimental data amenable to computerized search such that exact data from multiple articles can be searched/retrieved rapidly. 2. Digitization into a standard computer readable format would facilitate a seamless and semantic integration of data. 3. Data models for digitization of experimental data may be extended further to enable pre-publication integration of data. Thus, from the very beginning, the data would be in a format where it can be integrated into any database with minimal manual intervention. Such approach would help close the gap between the curated databases and the accumulated scientific literature. The manual curation workflow adopted in developing the database is designed to digitize the actual experimental data (presented as images or graphs) published in peer-reviewed articles. We developed a data curation workflow that was guided by the need to digitize experimental data as well as to lay foundation for development of standard representation of experimental data. In simple terms, every data-point in a graph or image represents data of several dimensions such as gene name, plant type, tissue and growth conditions. A combined systematic use of ontologies and notations has been done to represent information contained in every data point such that every data point is represented by a collection of these pre-defined terms. Since the notations are alphanumeric in nature with pre-defined definition, the data is stored in a relational database and can be easily searched and correlated. The current release of the database catalogues data for over 1800 rice genes from about 400 peer-reviewed research articles. Data from more than 4000 different experiments have been digitized using in-house developed manual data curation models. These experiments are based on a total of about 140 different experimental techniques mostly related to gene expression analysis, biochemical activity analysis, protein-protein interaction, DNA-protein interaction and cellular/sub-cellular localization. Since every aspect (gene id, tissue, growth conditions etc.) of the experimental data has been encoded with the help of defined notations (ontologies etc.) it is possible to retrieve the same set of data from several different perspectives. The database can be accessed either by browsing or searching for a particular keyword or term. A global overview of the data from different perspectives (PubMed id, gene/protein id, environmental/growth conditions, plant part/developmental stage or gene function and localization) can be acquired by "browsing" the database. Specific queries can be made by searching the database with the help of any of the ontology terms or with the help of a keyword. The database will be updated every 6 months and as the curation progresses the data would be enriched by inclusion of studies from diverse aspects such as biotic stress, yield etc. The ultimate aim is to digitize all the relevant articles but since the task is enormous we are proceeding in a methodical manner so that important aspects such stress biology (abiotic or biotic), yield are better represented.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://www.genomeindia.org/biocurationWebpage
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http://www.genomeindia.org/biocuration
metasource: Fairsharing.orgversion: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications:
Publications
More detailed information about this field from each metasource.
Manually curated database of rice proteins
PMID: 24214963
metasource: Fairsharing.org
version: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gkt1072
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Manually curated database of rice proteins
PMID: 24214963
metasource: Fairsharing.org
version: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gkt1072
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Manually curated database of rice proteins
PubMed citations: 12.
12 articles citing: Manually curated database of rice proteins
Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. PMID:34721467
Infrastructures of systems biology that facilitate functional genomic study in rice. PMID:30874968
Augmentation of crop productivity through interventions of omics technologies in India: challenges and opportunities. PMID:30370195
Identification of miRNA-mediated drought responsive multi-tiered regulatory network in drought tolerant rice, Nagina 22. PMID:29133823
RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response. PMID:28979289
A curated gluten protein sequence database to support development of proteomics methods for determination of gluten in gluten-free foods. PMID:28385663
Unraveling the molecular basis of oxidative stress management in a drought tolerant rice genotype Nagina 22. PMID:27716126
Microarray Analysis of Rice d1 (RGA1) Mutant Reveals the Potential Role of G-Protein Alpha Subunit in Regulating Multiple Abiotic Stresses Such as Drought, Salinity, Heat, and Cold. PMID:26858735
Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India. PMID:26743769
Information Commons for Rice (IC4R). PMID:26519466
Differentially expressed seed aging responsive heat shock protein OsHSP18.2 implicates in seed vigor, longevity and improves germination and seedling establishment under abiotic stress. PMID:26442027
Prioritization of candidate genes in QTL regions based on associations between traits and biological processes. PMID:25492368 - http://dx.doi.org/10.1093/nar/gkt1072
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annotation
metasource: Fairsharing.org
version: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
biocuration
metasource: Fairsharing.org
version: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
curated information
metasource: Fairsharing.org
version: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
digital curation
metasource: Fairsharing.org
version: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
literature curation
metasource: Fairsharing.org
version: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein interaction
metasource: Fairsharing.org
version: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
plant databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
rice
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
biocuration
metasource: Fairsharing.orgversion: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
curated information
metasource: Fairsharing.orgversion: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
digital curation
metasource: Fairsharing.orgversion: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
literature curation
metasource: Fairsharing.orgversion: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: MCDRP; Manually Curated Database of Rice Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qv0f6x; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
plant databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
rice
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
biocuration digital curation literature curation protein protein interaction plant rice
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