How to access the data

The data can be accessed in two ways:
1. Browse
 The in-house developed data curation models provide uniform structure to the experimental data originating from various experimental setups and thus provides a seamless integration of the data irrespective of the experimental technique. Thus, one can browse through the entire database from several different perspectives. One can start to browse either from research article id (PubMed id), rice protein id, plant part/developmental stage, environmental condition, phenotypic / biochemical trait, protein function, subcellular localization etc.

(a) Browse by PubMed id: Browsing with PubMed id would give a list of all the research articles that have been curated in the current release of the database. ‘Clicking’ on a particular ‘id’ would give the list of all the rice proteins studied in that article as well as all the experiments conducted in that article. Selecting a particular rice protein would open a page that summarizes the experimental data available for the protein. It would show all the relevant GO terms as well as all the tissue/developmental stages and environmental stages where the protein has been studied. A list of all the traits that have been associated with that protein by way of wet-lab work is also shown. Selecting any of these would take the user to the related digitized experimental data.  On the other hand, selecting a particular experiment would directly show the entire digitized data of the selected experiment. Kindly note that browsing the data with a PubMed id would initially restrict the data to only that article. However, if one wishes to access the data for the selected rice protein from the entire database, the option   ‘Search entire database for LOC_....’ on the top right of the ‘Locus id detail’ page should be used.
(b) Browse by either PO, EO, TO or GO term:  The database can also be browsed on the basis of any of the above mentioned terms. On selecting any of these choices a list of all the rice protein ids that have been experimentally studied in relation to the selected PO, EO, TO or GO term would be shown. Moving further through the links one gets to the actual digitized experimental data.

  • Plant Ontology term: to access data for a particular plant tissue or developmental stage.
  • Environmental Ontology term: to access data related to environmental conditions such as temperature, water status (drought), light or any chemical such as hormones, metal ions, etc.
  • Trait Ontology term: to access data related to any physical trait such as plant height, root length, no. of tillers as well as biochemical enzymatic activity such as kinase activity etc.
  • Gene Ontology term: to access data related to any molecular function such as DNA binding activity, antioxidant activity etc. or biochemical process such as signaling, response to stimulus etc. or cellular component such as localization to membrane, extracellular matrix etc.

2. Search
The database can also be searched by research article id (PubMed id), protein id, plant part/developmental stage (PO term), environmental condition (EO term), trait (TO term), protein function / localization (Gene Ontology). The search can be done by either the ‘ontology term id’ or any key word. If the search is done based on a keyword then data for all the related ontology terms would be shown. The appropriate data can then be selected.