Welcome to the CarboGrove Database API!
The CarboGrove API offers programmatic access to the data contained within the database. Using the API you can get information about the glycan binding proteins
for which we have data available, search and retreive the available analyzed datasets, search and retreive individual datasets, and obtain glycan binding protein affinity for many motifs.
Each of these functions accept GET parameters and return accessible JSON objects to facilitate programmatic access via curl or any other webreader.
To get a list of the available glycan binding proteins for which we have data and view associated metadata including uniprot ID's the following request returns the current list. This
function takes an optional "search" parameter to filter results by keyword. The "search" parameter is compared to a list of aliases and will match if the parameter is found in any of the aliases for a glycan binding protein.
This function returns list of glycan binding protein entries with fields for glycan binding protein name, species, protein family, common name, PFAM ID, and uniprot ID.
To search for available results use the following request with GET parameters "keysearch" "Sample_Provider" "Protein_Family" "Model Complexity" "Model_Source" and "Sort_Motif". Parameters
may be left blank. "keysearch" is compared to a list of aliases and will match if the parameter is found in any of the aliases for a glycan binding protein. All other parameters must be
an exact match, see advanced search
for lists of all parameter options.
This function returns list of results with fields including those returned for the list_gbp function as well as ResultID, source information (provider and catelogue number), and data used (DataID, Concentration, and Source)
To get the results for a specific ResultID in JSON format the following function can be used. This function requires a GET parameter "resultid"
This function returns two fields, "Motifs" which contains the details of the motifs produced by MotifFinder for this result, and "Data" which returns all the data used in the analysis as well
as the motif assignment produced by MotifFinder.
To search the available datasets in CarboGrove by glycan binding protein or data source the following function can be used. This function takes two optional GET parameters "search" and "source".
The "search" parameter is compared to a list of aliases and will match if the parameter is found in any of the aliases for a glycan binding protein. The "source" parameter is compared to the available data sources.
This function returns list of datasets giving glycan binding protein name, provider, concentration, and reference information.
To get the available data for a specific DataID the following function can be used. This function requires a GET parameter "dataid"
This function returns the data for a dataset as specified by dataid. This data is returned as list of columns for ids, raw and processed text, binding intensity, and standard deviation.
Note: For those interested in all the availabled data, rather than individually requesting each available dataset in a loop, we would politely ask that users simply download the complete via FigShare below.
This data is given as three tables with links between them to contain all the data.
To get the apparent affinity of each result for different motifs (used in motif-sort function for normal searching) the following function can be used:
This function returns the apparent affinity of result to glycans with a motif both as the fitted result (AvgRelativeBinding, Precision, and MotifScore) as well as the actual observed result
(AvgObservedBinding and ObservedMotifScore). The major difference is fitted results are extrapolated beyond the training glycans to all glycans in the database. This data is returned as list of columns.
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