Stress Combinations and their Interactions in Plants (SCIP) Database

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SCIP database - FAQ


What is SCIPDb (Stress Combination and their Interaction in Plants)?

  • SCIPDb is a compendium of the morpho-physiological (phenome) and molecular (transcriptome) responses of plants to different forms of combined stresses. The database hosts comprehensively analyzed literature- on the impact of different biotic and abiotic stress combinations on plants. SCIPDb is developed to provide the plant science researchers a user-friendly, easy-to-access computational platform integrated with diverse datasets and tools needed for data preparation, visualization, and - extraction for biological discovery in the area of combined stress.

What are the different datasets hosted in SCIPDb?

SCIPDb hosts two major combined stress datasets, namely,

  1. Phenome dataset that contains morpho-physiological, biochemical combined stress datasets.

  2. Transcriptome dataset containing microarray and RNA-seq datasets.

Is the data in the SCIPDb public?

  • Yes, all data in the SCIPDb is publically available for academic purposes.

    • What information does SCIPDb provide related to combined stresses?

    The SCIPdb acts as a resource reservoir for scientists, researchers and students trying to understand the impact of combined stresses on plants. Broadly the database provides the following information:
  • SCIPDb-Phenome provides information on the impact of combined stresses on growth, yield, morpho-physiological, biochemical, and pathogenesis related parameters of different plant species.
  • SCIPDb-Trancriptome analysis provides list of differentially expressed genes under combined stress and, their annotation, transcript levels, and pathway information. It also provides, information on co-expression network analysis, and gene-enrichment analysis of genes uniquely expressed under combined stress.
  • SCIPdb also hosts infromation on effect of combined stress on various genotypes of plants (wherever applicable) thus highlighting the genotype dependent impact of the combined stress.
  • The database hosts a comprehensive list of combined stress related traits which can be used for trait-based breeding programme to develop or identify combined stress tolerant plant species.
  • SCIPdb hosts for the first time the global geographical distribution of stress combinations and their impact on plant growth and productivity.
  • SCIPdb provides an comprehensive stress matrix and thus gives an idea about the most and least deleterious stress combination and plant species which are highly affected.

    • What can be downloaded from the database?

  • Users can download research materials (processed datafiles) and academic teaching materials from the download section of the database. The data provided SCIPDb should be used only for non-commercial and academic purposes only. Comprehensive information presented in the database has been fully credited with proper citation. The full-length references of all the articles hosted in the database are listed under the ‘reference & links’ tab. The main copyright for the data is held by the respective journals and the authors of the articles. The copyright for the analysed data presented as an application in the database is owned by SCIPDb. When using any information or data from the database, the users should cite both the database and the original source of the data (if applicable).

    • How to download the data in SCIPDb?

  • All data in SCIPDb are freely accessible for download in the Download section.
  • SCIPDb hosts an FTP server for the users to directly download all the raw data onto their local system. Data have been organised based on type of treatments (Sequential or Simultaneous), and then based on stress combination, to facilitate easy and convenient access for the users.
  • Files that can be downloaded include, processed phenomics data files, references, genotype/cultivar/variety data if present for a particular plant species.
  • Teaching materials like thesis, slides and posters are also hosted in SCIPdb. Please visit the download section for further details.
  • User-defined download can also be done, in specific sections of database.
  • Transcriptome data can be downloaded by selection of stress combination in the Transcriptome page of the datapage. Link to download transcriptome mutant data have been provided in downloads page itself.

    • How is the literature mining, sorting, and data analysis done?

  • The stepwise details have been explained in the Methodology-Phenome and Methodology-Transcriptome sections, respectively.
  • Briefly, the available articles under combined stress were retrieved using different kind of keywords. The keywords search was performed using search engines. After retrieving all the articles, we sorted the literature as ‘main’ and ‘ancillary’ articles based on their type (research, review, reports etc.) and the data contained (morpho-physiological).
  • The main research articles were considered for data extraction whereas reports, thesis, book chapters, abstracts, reviews, gene overexpression, and gene-silencing studies were listed under ancillary articles. All the articles related to physiological data were integrated into the database under ‘phenomics’ tab.
  • While analysing the information present in the ‘main’ research articles, parameters studied therein were listed and classified into type A, B, and C based on their significance in reflecting the net impact of stress.
  • Articles with transcriptome study were anaysed and integrated into the database under ‘transcriptome tab’.

    • Can I submit my data to SCIPDb?

  • If you have datasets related to combined stress in plants, and would like to submit them to SCIPDb, please go to Submit Page.

    • What is the copyright information about data hosted in SCIPDB?

  • The data presented in the SCIPDb is meant for promoting science and enriching combined stress research. The data provided herein should be used only for non-commercial and academic purposes.
  • We have taken care to prevent any copyright infringement. The main copyright for the data is held by the respective journals and the authors of the articles.
  • The copyright for the analyzed data presented as an application in the database is owned by SCIPDb.
  • When using any information or data from the database, the users should cite both the database and the original source of the data (if applicable).
    • Click here for copyright details

    How to contact the authors?

  • SCIPdb is developed by Muthappa Senthil-Kumar’s lab at NIPGR New Delhi.
  • Users can send their comments, queries, inputs and suggestions at scipdatabase@nipgr.ac.in or skmuthappa@nipgr.ac.in. Users can find the information under the Connect section. (Connect> Reach us).

    • The final outcome of combined stress is a complex and multifactorial process that depends on several factors. How does SCIPDb accounts for such variation and presents the impact of particular stress combination on plants from different literature studies?

  • We acknowledge that the impact of stress combination would depend on a number of factors like plant age, genotype, stress intensity, duration of the stresses, order of stress perceived by the plant, and time of initiation of subsequent stress since the first stress.. To emphasize this, we have presented the information on the factors (development stage, stress timing and stress order) on the data pages. Click here to view an example data page. Also, each study is analysed individually. For some of the studies where the impact varied with the stress intensity and stress order perceived by the plant, scroll bars are given to highlight the fact and the same information is also presented in tables and in inference section of data page. While making stress matrix and just to make generic sense out of the compiled data we have combined the different literature and made conclusions out of it considering the individual study outcome. However, we acknowledge that the response may vary as given in the individual data pages. All the detailed information is presented in the data pages. Also, to highlight that the impact may vary with genotypes, separate links in the data page for genotypes have been presented.
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