BiologicalNetworks BiologicalNetworks

API XML-RPC

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Common Data Types. 2

Common Structures. 2

Integrome DB functions. 4

Keyword search. 4

find list of objects by keyword(s). 4

find object(s) by keyword, organism.. 4

find object(s) by keyword, organism, type. 4

find publication(s)by keyword(s). 4

Curated pathways search. 5

list gene names by KEGG pathway. 5

list gene names by KEGG map and organism.. 5

list gene objects by KEGG pathway. 5

list gene objects by KEGG map and organism.. 5

find KEGG pathways by keyword(s). 6

find other curated pathways by keyword(s). 6

Object functions. 6

list top properties for object. 6

list all properties for object. 7

list top synonyms for object. 7

list all synonyms for object. 7

find neighbors (objects) by object. 7

list experiments for object. 8

find co-expressed objects for object. 8

list annotated terms by object and ontology. 8

Two and more objects functions. 8

find direct interactions between two objects. 8

find direct interactions inside group of objects. 9

find direct interactions between two groups of objects. 9

find shortest path between two objects. 9

find shortest path inside group of objects. 9

find shortest path between two groups of objects. 10

find neighbors for group of objects. 10

list experiments by group of objects. 10

find experiments by two co-expressed objects. 10

find experiments by group of objects where co-expressed. 11

Sequence DB functions. 11

list chromosomes for organism name. 11

get resources by organism name and chromosome name. 11

get resource by resource_id. 11

get sequence by resource, start, end. 12

find features by keyword(s). 12

find features corresponding to integrome DB object. 12

list feature types for resource. 13

get all features by resource[, start, end[ and type]]. 13

list of all features inside or overlapping interval of given feature[of specified type]. 13

Java integration example. 14

Source code. 14

 

Common Data Types

  • array -- Array of values, storing no keys
  • string -- string of characters, must follow XML encoding
  • struct -- associative array
  • base64 -- base64 encoded binary data
  • boolean -- logical value (0 or 1)
  • date/time -- Date and time in ISO 8601 format
  • double -- double precision floating point number
  • integer -- Whole number, integer
  • nil -- discriminative null value

Common Structures

1.      struct object (

        string id

        string name

        string type

)

 

2.      struct publication (

        string publication_id

        string contents

)

 

3.      struct pathway (

        string pathway_id

        string pathway_name

        string pathway_type

)

 

4.      struct property (

        string name

        string value

)

 

5.      struct experiment (

        string id

        string name

)

 

6.      struct edge (

        struct object start

        struct object connector

        struct object end

)

 

7.      struct seq_resource (

        string resource_id

        string resource_name

        string resource_length

)

 

8.      struct seq_feature (

        string feature_id

        string feature_name

        string feature_type

        string resource_id

        string start

        string end

)

 

All structures described above are represented by HashMap container. Please use property name as a key to access value in map for clients written in Java.

Integrome DB functions

Keyword search

find list of objects by keyword(s)

This function retrieves all objects (e.g. proteins, genes, small molecules, experiments, etc.) for the set of terms/keywords. Terms/keywords can be gene/protein names (e.g. "p53") as well as general terms (e.g. "apoptosis")

         Method signature

array Integrome.find ( string keywords )

         Parameters

string keywords - comma separated list of keywords

         Result

array of objects

find object(s) by keyword, organism

This function retrieves all objects (e.g. proteins, genes, small molecules, experiments, etc.) for the set of terms/keywords in particular organism. Terms/keywords can be gene/protein names (e.g. "p53") as well as general terms (e.g. "apoptosis")

         Method signature

array Integrome.find ( string keywords, string organism_name )

         Parameters

string keywords - comma separated list of keywords

string organism_name - canonical organism name, nil value removes this filter,

         Result

array of objects

find object(s) by keyword, organism, type

This function retrieves all objects of a specified type (e.g. 'proteins') only for the set of terms/keywords in particular organism(s). Terms/keywords can be gene/protein names (e.g. "p53") as well as general terms (e.g. "apoptosis")

         Method signature

array Integrome.find ( string keywords, string organism_name, string object_type )

         Parameters

string keywords - comma separated list of keywords

string organism_name - canonical organism name, nil value removes this filter,

string object_type - type (from predefined list) , nil value removes this filter

         Result

array of objects

find publication(s) by keyword(s)

This function retrieves all publications for the set of terms/keywords. Terms/keywords can be gene/protein names (e.g. "p53") as well as general terms (e.g. "apoptosis")

         Method signature

array Integrome.find _publication ( string keywords )

         Parameters

string keywords - comma separated list of keywords

         Result

array of publications

Canonical pathways search

list gene names by KEGG pathway

This function returns a list of genes that are containing in a specified KEGG pathway. KEGG pathway is specified by KEGG pathway ID (e.g. "hsa05213")

         Method signature

array Integrome.get_genes_by_pathway ( string pathway )

         Parameters

string pathway pathway name

         Result

string array of gene names

list gene names by KEGG map and organism

This function returns a list of genes that are containing in a specified KEGG pathway. KEGG pathway is specified by KEGG pathway map ID (e.g. "map00010") and organism (e.g. "homo sapiens")

         Method signature

array Integrome.get_genes_by_pathway ( string keggmap, string organism )

         Parameters

string keggmap kegg map name (like map00010)

string organism - canonical organism name

         Result

string array of gene names

list gene objects by KEGG pathway

This function returns a list of gene objects that are containing in a specified KEGG pathway. KEGG pathway is specified by KEGG pathway ID (e.g. "hsa05213")

         Method signature

array Integrome.get_genes_by_pathway ( string pathway )

         Parameters

string pathway pathway name

         Result

array of objects

list gene objects by KEGG map and organism

This function returns a list of gene objects that are containing in a specified KEGG pathway. KEGG pathway is specified by KEGG pathway map ID (e.g. "map00010") and organism (e.g. "homo sapiens")

         Method signature

array Integrome.get_genes_by_pathway ( string keggmap, string organism )

         Parameters

string keggmap kegg map name (like map00010)

string organism - canonical organism name

         Result

array of objects

find KEGG pathways by keyword(s)

This function returns a list of KEGG pathways that are most relevant to provided keywords/terms. The keywords can be gene names as well as general keywords from pathways description (e.g. "apoptosis")

         Method signature

array Integrome.find _kegg_pathways ( string keywords )

         Parameters

string keywords - comma separated list of keywords

         Result

array of pathways

find other canonical pathways by keyword(s)

This function returns a list of canonical pathways from NCI/Nature, Reactome, Wiki, Imaging pathways databases that are most relevant to provided keywords/terms.
The keywords can be gene names as well as general keywords from pathways description (e.g. "apoptosis")

         Method signature

array Integrome.find _curated_pathways ( string keywords, string type )

         Parameters

string keywords - comma separated list of keywords

string type - type (from the list of NCU/Nature, Reactome, Wiki, Imaging pathways), nil value removes this filter

         Result

array of pathways

 

Object functions

list top properties for object

This function returns most popular properties for an object (gene, protein, drug, etc.). Most popular properties are defined as properties most widely used in public databases (e.g. Description, Function, Synonyms)

         Method signature

array Integrome.get_top_properties( string object_id)

         Parameters

string object_id object id

         Result

array of properties

list all properties for object

This function returns ALL properties for an object (gene, protein, drug, etc.).

         Method signature

array Integrome.get_all_properties( string object_id)

         Parameters

string object_id object id

         Result

array of properties

list top synonyms for object

This function returns most popular synonyms for an object (gene, protein, drug, etc.). Most popular synonyms are defined as synonyms most widely used in public databases (e.g. "TP53" for a "p53")

         Method signature

array Integrome.get_top_synonyms ( string object_id)

         Parameters

string object_id object id

         Result

array of string

list all synonyms for object

This function returns ALL synonyms for an object (gene, protein, drug, etc.).

         Method signature

array Integrome.get_all_synonyms ( string object_id)

         Parameters

string object_id object id

         Result

array of string

find neighbors (objects) for an object

This functions returns a list of objects (genes, proteins, small molecules, etc.) that have at least one relation (e.g. protein-protein interaction, co-citation, genetic interaction) with a given object.

         Method signature

array Integrome.find_neighbors ( string object_id)

         Parameters

string object_id object id

         Result

array of objects

list of experiments for an object

This function returns a list of experiments (e.g. microarray gene expression) that contain a given object (gene, protein, metabolite, etc.)

         Method signature

array Integrome.find_experiments ( string object_id)

         Parameters

string object_id object id

         Result

array of experiments

find co-expressed objects for an object

This function returns "co-expressed" (or correlating in time) genes, proteins, metaboites retrieved from integrated gene expression, proteomics and metabolomics experiments for an object (gene, protein, metabolite)

         Method signature

array Integrome.find_coexpressed_objects ( string object_id)

         Parameters

string object_id object id

         Result

array of objects

list annotated ontology terms for an object

This function returns a list of GeneOnotlogy annotations for a gene/protein

         Method signature

array Integrome.get_terms( string object_id)

         Parameters

string object_id object id

         Result

array of string

Two and more objects functions

find direct interactions between two objects

This function returns a list of direct interactions (protein-protein, protein-dna, genetic, etc) for two objects (gene, protein, small molecule, etc.)

         Method signature

array Integrome.find_direct_interactions (string object_1_id, string object_2_id)

         Parameters

string object_1_id first object id

string object_2_id second object id

         Result

array of edges

find direct interactions inside group of objects

This function returns a list of direct interactions (protein-protein, protein-dna, genetic, etc) for a group (>2) of objects (gene, protein, small molecule, etc.)

         Method signature

array Integrome.find_direct_interactions (array string object_ids)

         Parameters

array string object_ids first group of object ids

         Result

array of edges

find direct interactions between two groups of objects

This function returns a list of direct interactions (protein-protein, protein-dna, genetic, etc) for two groups of objects (gene, protein, small molecule, etc.)

         Method signature

array Integrome.find_direct_interactions (array string object_1_ids, array string object_2_ids)

         Parameters

array string object_1_ids first group of object ids

array string object_2_ids second group of object ids

         Result

array of edges

find shortest path between two objects

This function finds shortest interaction path between two objects (genes, proteins, small molecules, etc.)

         Method signature

array Integrome.find_direct_interactions (string object_1_id, string object_2_id)

         Parameters

string object_1_id first object id

string object_2_id second object id

         Result

array of edges

find shortest paths inside group of objects

This function finds shortest interaction paths among group (>2) of objects (genes, proteins, small molecules, etc.)

         Method signature

array Integrome.find_direct_interactions (array string object_ids)

         Parameters

array string object_ids first group of object ids

         Result

array of edges

find shortest paths between two groups of objects

This function finds shortest interaction path between two groups of objects (genes, proteins, small molecules, etc.)

         Method signature

array Integrome.find_direct_interactions (array string object_1_ids, array string object_2_ids)

         Parameters

array string object_1_ids first group of object ids

array string object_2_ids second group of object ids

         Result

array of edges

find neighbors for group of objects

This function finds objects (genes, proteins, small molecules, etc.) that have at least one relation/interaction (e.g. protein-protein interaction, co-citation) with a group of objects

         Method signature

array Integrome.find_direct_interactions (array string object_ids)

         Parameters

array string object_ids first group of object ids

         Result

array of edges

list experiments by group of objects

This function returns a list of experiments (e.g. gene expression, metabolomics) that contain at least one object from a group of objects

         Method signature

array Integrome.find_coexpressed_objects (array string object_ids)

         Parameters

array string object_ids group of object ids

         Result

array of experiments

find experiments by two co-expressed objects

This function returns a list of experiments (e.g. gene expression, metabolomics) in which given objects are coexpressed (corellating in time)

         Method signature

array Integrome.find_experiments_of_coexpressed_objects (string object_1_id, string object_2_id)

         Parameters

string object_1_id first object id

string object_2_id second object id

         Result

array of experiments

find experiments by group of objects where co-expressed

This function returns a list of experiments (e.g. gene expression, metabolomics) that contain at least one pair of co-expressed (coreelating in time values) objects from a group of objects

         Method signature

array Integrome.find_coexpressed_objects (array string object_ids)

         Parameters

array string object_ids group of object ids

         Result

array of experiments

Sequence DB functions

list chromosomes for organism name

This function returns a list of chromosomes for an organism (e.g. "homo sapiens")

         Method signature

array sequence.list_chromosomes(string organism_name)

         Parameters

string organism_name canonical organism name

         Result

array of strings

get resources by organism name and chromosome name

This function returns a list of resources (e.g. "Selera", "NCBI, "Ensembl") for an organism (e.g. "homo sapiens") and chromosome (e.g. "chr15")

         Method signature

array sequence.find_resources(string organism_name, string chromosome)

         Parameters

string organism_name canonical organism name

string chromosome canonical organism name, nil value removes the filter

         Result

array of resources

get resource by resource_id

This function returns a list of resources (e.g. "Selera", "NCBI, "Ensembl") by resource id

         Method signature

struct resource sequence.get_resources(string resource_id)

         Parameters

string resource_id sequence db internal resource identifier

         Result

struct resource

get sequence by resource, start, end

This function returns sequence for resource (specific chromosome in a specific genome) specified by ID by Start and End positions

         Method signature

string sequence.get_sequence(string resource_id, int start, int end)

         Parameters

string resource_id sequence resource id

int start start of region

int end end of region

         Result

string

find features by keyword(s)

This function for a list of keywords such as gene names, as well as general keyword (e.g. "apoptosis") returns a list of genomic sequence features (start/end position, promoter position, regulatory region/binding sites, and others) for returned genes

         Method signature

array sequence.find_features(string keywords, string type)

         Parameters

string keywords comma separated list of keywords

string feature_type feature type, nil value to disable this filter

         Result

array of features

find features corresponding to integrome DB object

This function for an ObjectID of the IntegromeDB object (e.g. gene) returns a list of genomic sequence features (start/end position, promoter position, regulatory region/binding sites, and others) for returned genes

         Method signature

array sequence.find_corresponding_features(string object_id)

         Parameters

string object_id object id from Integrome DB

         Result

array of features

list feature types for resource

This function for a resource id (providing chromosome id in a organism) returns a list of genomic sequence features (start/end position, promoter position, regulatory region/binding sites, and others) for returned genes

         Method signature

array sequence.list_feature_types(string resource_id)

         Parameters

string resource_id sequence resource id

         Result

array of string

get all features by resource[start, end and type]

This function for a resource id (providing chromosome id in a organism) and start, end positions of a genomic region returns a list of specified regions (e.g. binding sites) that are inside [start, end] region

         Method signature

array sequence.list_features(string resource_id, int start, int end, string feature_type)

         Parameters

string resource_id sequence resource id

int start start of region

int end end of region

string feature_type feature type, nil value to disable this filter

         Result

array of features

list of all features inside or overlapping interval of given feature [of specified type]

This function for a resource id (providing chromosome id in a organism) and start, end positions of a genomic region returns a list of specified regions (e.g. binding sites) that are inside or overlapping with the [start, end] region

         Method signature

array sequence.list_intersected_features(string feature_id, string feature_type, boolean inside_only)

         Parameters

string resource_id sequence resource id

string feature_type feature type, nil value to disable this filter

boolean inside_only- return only containing features if true, overlapping otherwise

         Result

array of features

 


 

Java integration example

This Java source code example shows the usage of find objects by keyword and organism and then list top synonyms for each object found. In order to let this example work you should have apache xml-rpc libraries linked to your project and available for download from http://ws.apache.org/xmlrpc/.

Source code

package xmlrpc_client;

import java.net.MalformedURLException;
import java.net.URL;
import java.util.Arrays;
import java.util.HashMap;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.apache.xmlrpc.XmlRpcException;
import org.apache.xmlrpc.client.XmlRpcClient;
import org.apache.xmlrpc.client.XmlRpcClientConfigImpl;
import org.apache.xmlrpc.client.XmlRpcCommonsTransportFactory;

/**
 * Test class to find objects by keyword and organism and then
 * list top synonyms for each of them
 @author Sergey Kozhenkov
 */
public class Main {
    public static void main(String[] args) {
        try {
            XmlRpcClientConfigImpl config = new XmlRpcClientConfigImpl();
            config.setServerURL(new URL("http://integromedb.org/integrome"));
            config.setEnabledForExtensions(true);
            XmlRpcClient client = new XmlRpcClient();
            // use Commons HttpClient as transport
            client.setTransportFactory(new XmlRpcCommonsTransportFactory(client));
            // set configuration
            client.setConfig(config);

            Object[] params = new Object[]{"p53""Homo sapiens"};
            Object[] result = (Object[]) client.execute("Integrome.find", params);
            if (result != null) {
                for (Object rec : result) {
                    HashMap<String, String> map = (HashMap<String, String>) rec;
                    long id = Long.parseLong(map.get("id"));
                    System.out.println("Object: " + map.get("name") + " (" + id + "), type: " + map.get("type") + ", organism: " + map.get("organism"));

                    params = new Object[]{"" + id};
                    Object[] synonyms = (Object[]) client.execute("Integrome.get_top_synonyms", params);
                    if (synonyms != null) {
                        System.out.println(Arrays.toString(synonyms));
                    }
                }
            }
        catch (MalformedURLException ex) {
            Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
        catch (XmlRpcException ex) {
            Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
        }
    }
}

BiologicalNetworks integration with external site

Download as Microsoft word document

Description

To establish integration with BiologicalNetwork you must put special link(s) on your web page(s) with all the required parameters according to this document. Also BiologicalNetwork must be installed on client’s machine in order to launch required routine and show the result inside application.

 

Navigating to this link will initiate special text file downloading with all required parameters. Downloading procedure brings system "Save & open dialog” with associated BiologicalNetwork application to handle this file type.

Functions

Show Interactions for object

·         Predefined link parameters

open – value “pathway

type – value “interactions

·         Variable link parameters

string – object name

·         Example: show interactions for P53 protein.

http://integromedb.org/params2xml?open=pathway&type=interactions&string=p53

Show Interactions for object with specified organism

·         Predefined link parameters

open – value “pathway

type – value “interactions

·         Variable link parameters

string – object name

organism – canonical organism name, all spaces encoded as “%20”

·         Example: show interactions for P53 protein.

http://integromedb.org/params2xml?open=pathway&type=interactions&string=p53&organism=Homo%20sapiens

Show Multi Experiment View for object

·         Predefined link parameters

open – value “mev

·         Variable link parameters

string – object name

·         Example: show multi-experiment viewer for P53 protein.

http://integromedb.org/params2xml?open=mev&string=p53

Show Multi Experiment View for object with specified organism

·         Predefined link parameters

open – value “mev

·         Variable link parameters

string – object name

organism – canonical organism name, all spaces encoded as “%20”

·         Example: show multi-experiment viewer for P53 protein.

http://integromedb.org/params2xml?open=mev&string=p53&organism=Homo%20sapiens

Show Sequence View for object

·         Predefined link parameters

open – value “sequence

type – value “sequencedb

·         Variable link parameters

string – object name

·         Example: show sequence for P53 protein.

http://integromedb.org/params2xml?open=sequence&string=p53

Show Sequence View for object in with specified organism

·         Predefined link parameters

open – value “sequence

type – value “sequencedb

·         Variable link parameters

string – object name

organism – canonical organism name, all spaces encoded as “%20”

·         Example: show sequence for P53 protein.

http://integromedb.org/params2xml?open=sequence&string=p53&organism=Homo%20sapiens