a. Interface design:
On the browse page, by clicking on the Legend button with blue filling, you will get the detailed interpretation of the graphical elements indicating the sorting feature of the proteins, and the colors used to symbolize the different evidence levels (evidencing experimental methods)
b. Entry sorting:
Clicking on one of the seven filter buttons below the Browse header, you can select the sought options in the pop-up menu by checking the corresponding checkboxes. These filters are:
Evidence level: experiments of the database were classified into 11 groups
Organ: The tissue where the experiments were conducted
Cell: Cell line used for experiments
Localization: subcellular localization of the protein
Species: orthologs were collected from 15 closely related species
Gene: gene associated for the protein for which experiments were carried out
Protein: protein participated in the experiment
If you want to list the displayed entries in a given order, you should select the Order by function, and click one or two times on the button before the proper parameter, to change its from none to ascending or descending.
Users can download PolarProtDB by clicking 'Download' in the left menu. Users can download different types of data (experiments, protein localization, alignments) in different formats (json, csv, xml, tab).
There are 3 different searching modes in PolarProtDB.
a. Searching in categories:
The right side of the main page contains multiple predefined browse options based on different levels - e.g. protein, gene, species and other.
Proteins: lists all proteins in PolarProtDB
Genes: lists all genes in PolarProtDB
Species: lists all species in PolarProtDB
Experiments: lists all proteins for which experiments were carried out
Organs: lists every organs for which experiments were performed
Cells: lists cell lines on experiments were conducted
Glycans: lists all glycans that were associated to any protein
b. Browsing in all entries and using filters:
At the same time users can browse between all entries by clicking on the browse button in the left menu. By applying various filters users can list their proteins of choice. For more details, see 1.b.
c. Search by keywords:
Users can also search using any term (gene name, protein name or accession, etc.) at the top of the page.
4. Entry viewer:
Once the user found the protein of his/her choice, every information related to that entry is listed.
On the top of the page, the gene name and the different experiments are displayed for the particular protein. Ortholog proteins are also listed.
In order to compare data from related proteins, multiple sequence alignment of orthologs together with mirrored structural and functional information is shown at the middle – topology, short linear motifs, intrinsically disordered regions, phosphorylation and glycosylation. Users can zoom on the bars to enlarge it and view the individual sequence.
At the bottom of the page exact region boundaries of all data for the particular protein are displayed.
5. Register and Log in:
Registration is required only for submission of new experimentals. All data in PolarProtDb can be accessed without an account.
If you are logged in to the database, select the Add experiments option in the Annotate drop-down list in the upper right corner of the page. To submit your data, click on the Add new experiment button and fill all the text boxes or choose the proper options from the lists in the pop-up window. Please, be careful to enter valid UniProt ID or AC as sequence identifier, otherwise your data would not be submitted for inspection. Until the acceptance, your last annotations will remain to be displayed with red background in the list of your experiments.
c. Dealing with your submitted annotation:
If you submitted an experiment, you can find a three buttons on the right of the corresponding line in your annotation list. By clicking on one of them, you can modify, or cancel your submission, or contact with the administrators. Researchers who annotate a great number of experiments in PolarProtDb will be invited to be co-authors of the publications of the subsequent updates.
If you are intended to reach the entries in PolarProtDb in a more dynamic way, you should use PolarProt API under the following URL: