PLAPID.ORG
A REFERENCE DATABASE FOR PLANT PROTEIN-PROTEIN INTERACTION

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HELP & FAQ
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  • What is PlaPID?
    • PlaPID (Plant Protein Interaction DataBase) is a searchable database for protein-protein interactions in plants. It associates high-confidence information derived from published literatures and several databases. PlaPID aims to provide a reference database and a simple access to plant PPIs for the bioinformatics community as well as the wet lab scientists. It contains protein interactions not only within plants, but also between plants and virus or bacteria. PlaPID will be timely updated.

  • How many species are included in PlaPID?
    • Currently, seven species which have drawn most attention in plants are included in PlaPID: Arabidopsis thaliana, rice (Oryza sativa), pea (Pisum sativum), wheat (Triticum aestivum), barley (Hordeum vulgare), corn (Zea mays) and tomato (Lycopersicon esculentum). In the future, we also intend to integrate more species into the database.

  • What is the background of the scientists involved in establishing PlaPID?
    • PlaPID has been established and maintained by a team in the bioinformatics lab, led by Dr. Xiao Li at Sichuan University.

  • How can I download data from the PlaPID database?

  • Is a license required to download and use the PlaPID data and/or applications?
    • There are no license conditions attached to the use of PlaPID. But before downloading datasets from our database, we recommend you to input your institution and related information first. Thank you!

  • Is the PlaPID Database interoperable?
    • Yes, all the information contained in this database will be available for downloading as XML and FLAT files. The PSI MI XML format is a data exchange format for protein-protein interactions. It is community standards for data representation in proteomics to facilitate data comparison, exchange and verification.

  • Are you using any literature mining algorithm?
    • We are not using any literature mining program. To ensure the data reliability, only those from published literatures or literature-based and experiment-based datasets are extracted.

  • Can I link to PlaPID?
    • We welcome and encourage you to provide links back to PlaPID from your database or program. For questions and comments, email us: lix@scu.edu.cn

  • How to query potential PPI pairs related with interested protein(s)?
    • You can access PPI information by querying one or more proteins. "Single Search" allows you to submit a single protein when you would like to know how many proteins have the probability to interact with the protein you have submitted. "Multiple search" allows you to query more than two proteins when you would like to get the interaction information among these proteins. Moreover, you can use one of the following types of protein ID to query: UniProtKB AC, Entrez GeneID, TAIR ID (Arabidopsis thaliana only), TIGR Locus ID, GI number and Gene Symbol.

  • What are included in returned page after query?
    • After you submit protein(s) in Query Page, basic protein information is returned, including protein ID, gene ID, number of interactions, functional annotations and database cross-references. PPI information is graphically displayed when you press the bottom "View Interaction Network Graphic". If you press one protein in the image, the page can be linked to the PPI information of this protein.

  • Can I submit protein interaction data to PlaPID?
    • PlaPID encourages submission of PPI in plants through web interface. The submitters can either upload a protein interaction file in PSI-MI format, or enter it directly in our web interface. After our validation, the interactions will be updated into our database.

  • What kinds of protein ID are included in PlaPID?
    • There are many kinds of protein ID included in PlaPID:
      TIGR ID: TIGR (The Institute for Genomic Research) has finished the complete annotation of the Arabidopsis thaliana and Oryza sativa genome to a uniform high standard. For more information please click here: http://www.tigr.org/index.shtml
      UniprotKB AC: UniprotKB is a curated protein sequence database which strives to provide a high level of annotation, a minimal level of redundancy and high level of integration with other databases. For more information please click here: http://expasy.org/sprot/
      Entrez GeneID: Entrez Gene is a searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer. For more information please click here: http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene
      GI number: GI number is simply a series of digits that are assigned consecutively to each sequence record processed by NCBI. For more information please click here: http://www.ncbi.nlm.nih.gov/sites/entrez?db=protein
      TAIR ID: TAIR (The Arabidopsis Information Resource) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. For more information please click here: http://www.arabidopsis.org