Programmatic access to Abasy Atlas is provided by a RESTful API based on the following URI structure:
https://abasy.ccg.unam.mx/rest/{dataset}/{regnetid}[?{query}]
The possible datasets are regnets, genes, complexes, modules, and modules/annot.
Requests have a rate limit of 10 requests/second.
query stringA query is a set of constrains separated by & symbols as follow:
{constraint}&{constraint}&...&{constraint}
Where each constraint comprises a parameter to which optionally can be assigned a single value or a set of values (separated by + symbols), according the following syntax:
{parameter}[={value}[+{value}+...+{value}]]
Each parameter must appear only once in a query. The possible parameters and values are specific to each dataset as described below.
format parameterThe format parameter can be used with all the datasets, and its possible values can be json (the default if format is omitted) or text for tab-separated values. The response representations for these formats are 'Content-Type: application/json' and 'Content-Type: text/plain', respectively. The text format provides by default a table header that can be suppressed by appending the no_header parameter.
regnets datasetThe parameter field is required to query an assortment of different properties for a regulatory network. When only a regnetid with no field parameter is provided, the regulatory network annotated with the classes of the NDA encoded as JSON format is retrieved.
The possible values for the field parameter are as follow:
Values for the field parameter |
||
|---|---|---|
Network_nodes | – | Number of nodes |
Num_nonleaf_nodes | – | Number of regulators |
Num_leaf_nodes | – | Number of non-regulators |
Num_Edges | – | Number of undirected interactions |
Num_Arcs | – | Number of directed interactions |
Num_Selfloops | – | Number of self-regulations |
Max_Kout | – | Maximum out-connectivity |
Num_weak_comp | – | Number of weak components |
Network_density | – | Fraction of directed interactions relative to all the possible interactions (n2) |
Num_nodes_biggest_comp | – | Number of nodes in the giant component |
Regnet_name | – | Name of the regulatory network |
Regnet_id | – | ID of the regulatory network |
Num_FFs | – | Number of feedforward motifs |
Num_CFFs | – | Number of complex-feedforward motifs |
Num_3FBLs | – | Number of 3-feedback circuits |
Avg_short_path_length | – | Average shortest path length |
Network_diameter | – | Diameter of the network |
Avg_clus_coeff | – | Average clustering coefficient |
Pk_coeff | – | Coefficient of the degree distribution |
Pk_exponent | – | Exponent of the degree distribution |
Pk_r_square | – | Goodness of fit for the degree distribution |
Pkout_coeff | – | Coefficient of the out-degree distribution |
Pkout_exponent | – | Exponent of the out-degree distribution |
Pkout_r_square | – | Goodness of fit for the out-degree distribution |
Ck_coeff | – | Coefficient of the clustering distribution |
Ck_exponent | – | Exponent of the clustering distribution |
Ck_r_square | – | Goodness of fit for the clustering distribution |
Kappa | – | κ-value | global regulators are those nodes having an out-degree (kout) > κ-value |
genes, complexes, modules, and modules/annot datasetsNo additional parameters are available for these datasets.
Regulatory protein complexes of Escherichia coli version 2005 in JSON:
https://abasy.ccg.unam.mx/rest/complexes/511145_v2005_sRDB04?format=json
Regulatory protein complexes of Escherichia coli version 2005 in tab-separated values:
https://abasy.ccg.unam.mx/rest/complexes/511145_v2005_sRDB04?format=text
Regulatory protein complexes of Escherichia coli version 2005 in tab-separated values without header:
https://abasy.ccg.unam.mx/rest/complexes/511145_v2005_sRDB04?format=text&no_header
List of all the modules in Escherichia coli version 2005 in JSON by default (no format parameter):
https://abasy.ccg.unam.mx/rest/modules/511145_v2005_sRDB04
Module annotations of Escherichia coli version 2005 in JSON:
https://abasy.ccg.unam.mx/rest/modules/annot/511145_v2005_sRDB04?format=json
Some structural properties of Escherichia coli version 2005 in JSON:
https://abasy.ccg.unam.mx/rest/regnets/511145_v2005_sRDB04?field=Regnet_id+Network_nodes+Num_arcs+Num_selfloops+Avg_clus_coeff&format=json
Regulatory network of Escherichia coli version 2005 encoded as JSON by default (no field nor format parameters):
https://abasy.ccg.unam.mx/rest/regnets/511145_v2005_sRDB04
