Web Service: copub

Target Namespace:
http://services.nbic.nl/copub

Port copubSOAP Port typeSource code

Location:
http://services.nbic.nl/copub5/api/soap11
Protocol:
SOAP
Default style:
document
Transport protocol:
SOAP over HTTP
Operations:
  1. get_categoriesDetailSource code
  2. get_chipsDetailSource code
  3. get_enriched_keywordsDetailSource code
  4. get_genesDetailSource code
  5. get_keywordsDetailSource code
  6. get_literature_neighboursDetailSource code
  7. get_literature_networkDetailSource code
  8. get_referencesDetailSource code
  9. selftestDetailSource code
  10. versionDetailSource code

Operations

    Port type copubSource code

    1. get_categories
      Description:
      Fetch the list of categories. Note: Not all categories can be used everywhere, use purpose to get the right categories
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      http://services.nbic.nl/copub/get_categories
      Input:
      get_categoriesRequest (soap:body, use = literal)Source code
      parameters type get_categories
      • purpose - optional; type purposeType - type string with restriction - enum { 'enrichment', 'keyword', 'neighbour' }
        Default is enrichment
      Output:
      get_categoriesResponse (soap:body, use = literal)Source code
      parameters type get_categoriesResponse
      • categories type CategoriesType
        • category - unbounded; type string
    2. get_chips
      Description:
      Retrieve list of chips
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      http://services.nbic.nl/copub/get_chips
      Input:
      get_chipsRequest (soap:body, use = literal)Source code
      parameters type get_chips
      • gene_identifier_type - optional; type gene_identifier_typeType1 - type string with restriction - enum { 'affymetrix' }
        Choice is affymetrix. Default affymetrix
      Output:
      get_chipsResponse (soap:body, use = literal)Source code
      parameters type get_chipsResponse
      • chips type chipsType
        • chip - unbounded; type string
    3. get_enriched_keywords
      Description:
      Calculates keyword overrepresentation in a set of regulated genes (literature based).
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      http://services.nbic.nl/copub/get_enriched_keywords
      Input:
      get_enriched_keywordsRequest (soap:body, use = literal)Source code
      parameters type get_enriched_keywords
      • categories type CategoriesType
        • category - unbounded; type string
      • gene_identifiers type GeneIdentifiersType
        • gene_identifier - unbounded; type string
      • gene_identifier_type - optional; type gene_identifier_typeType - type string with restriction - enum { 'entrezgene', 'affymetrix', 'ensemblgene' }
        Default is entrezgene
      • chip - optional; type string
        When gene_identifier_type is affymetrix this is the chip name
      • gene_number_threshold - optional; type int
      • literature_count_threshold - optional; type int
      • p_value_threshold - optional; type float
        Maximum of 1
      • r_scaled_score_threshold - optional; type float
      • gene_orthology_selection - optional; type gene_orthology_selectionType - type string with restriction - enum { 'Cross-species', 'Species-specific' }
        Default is Cross-species
      Output:
      get_enriched_keywordsResponse (soap:body, use = literal)Source code
      parameters type get_enriched_keywordsResponse
      • nr_of_gene_identifiers type int
      • nr_of_genes type int
      • total_nr_of_enriched_keywords type int
      • enriched_keywords type EnrichedKeywordsType
        • enriched_keyword - optional, unbounded; type EnrichedKeywordType
          • bi_id type int
          • preferred_name type string
          • alternative_names - optional; type alternative_namesType
            • alternative_name - optional, unbounded; type string
          • category type string
          • gene_count type int
          • p_value type float
          • genes type literature_neighboursType
            Genes which make current keyword enriched
            • literature_neighbour - optional, unbounded; type literature_neighbourType
              • bi_id type int
              • preferred_name type string
              • alternative_names - optional; type alternative_namesType
                • alternative_name - optional, unbounded; type string
              • entrezgene_id - optional; type int
              • symbol - optional; type string
              • aliases - optional; type aliasesType
                • alias - optional, unbounded; type string
              • organism - optional; type organismType - type string with restriction - enum { 'human', 'mouse', 'rat', 'any' }
                human mouse or rat
              • affymetrix_ids - optional; type affymetrix_idsType
                • affymetrix_id - optional, unbounded; type string
              • ensembl_id - optional; type string
              • literature_count type int
              • r_scaled_score type float
    4. get_genes
      Description:
      Search by gene symbol or name or entrezgene/ensembl/affymetri id Return list of genes
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      http://services.nbic.nl/copub/get_genes
      Input:
      get_genesRequest (soap:body, use = literal)Source code
      parameters type get_genes
      • query type string
        Query is exact. Use * as wildcard
      • query_type - optional; type query_typeType - type string with restriction - enum { 'symbol', 'name', 'entrezgene', 'ensemblgene', 'affymetrix' }
        Choices symbol, name, entrezgene, ensemblgene, affymetrix. Default name
      • organism - optional; type organismType - type string with restriction - enum { 'human', 'mouse', 'rat', 'any' }
        Choices are human, mouse, rat or any. Default human
      • max_results - optional; type int
        Maximum number of hits per bi_id and category to return Default is 50 Max is 1000
      Output:
      get_genesResponse (soap:body, use = literal)Source code
      parameters type get_genesResponse
      • genes type GenesType
        • gene - optional, unbounded; type GeneType
          • bi_id type int
          • preferred_name type string
          • alternative_names - optional; type alternative_namesType
            • alternative_name - optional, unbounded; type string
          • entrezgene_id type int
          • symbol - optional; type string
          • aliases - optional; type aliasesType
            • alias - optional, unbounded; type string
          • organism - optional; type organismType - type string with restriction - enum { 'human', 'mouse', 'rat', 'any' }
            human, mouse or rat
          • affymetrix_ids - optional; type affymetrix_idsType
            • affymetrix_id - optional, unbounded; type string
          • ensembl_id - optional; type string
    5. get_keywords
      Description:
      Search for a keyword in a category Return list of keyword
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      http://services.nbic.nl/copub/get_keywords
      Input:
      get_keywordsRequest (soap:body, use = literal)Source code
      parameters type get_keywords
      • query type string
        Query is exact. Use * as wildcard
      • category type string
      • max_results - optional; type int
        Maximum number of keywords to return Default is 50 Max is 1000
      Output:
      get_keywordsResponse (soap:body, use = literal)Source code
      parameters type get_keywordsResponse
      • keywords type KeywordsType
        • keyword - optional, unbounded; type KeywordType
          • bi_id type int
          • preferred_name type string
          • alternative_names - optional; type alternative_namesType
            • alternative_name - optional, unbounded; type string
    6. get_literature_neighbours
      Description:
      Find the literature neighbours of a gene/keyword in a category
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      http://services.nbic.nl/copub/get_literature_neighbours
      Input:
      get_literature_neighboursRequest (soap:body, use = literal)Source code
      parameters type get_literature_neighbours
      • bi_ids type bi_idsType
        • bi_id - unbounded; type int
      • categories type CategoriesType
        • category - unbounded; type string
      • max_results - optional; type int
        Maximum number of hits per bi_id and category to return Default is 50 Max is 1000
      • literature_count_threshold - optional; type int
      • r_scaled_score_threshold - optional; type int
      • sortdir - optional; type neighbourSortType - type string with restriction - enum { 'r_scaled_score:DESC', 'r_scaled_score:ASC', 'literature_count:DESC', 'literature_count:ASC' }
        Order of neighbours. Can be r_scaled_score|literature_count:DESC|ASC. Default is r_scaled_score:DESC.
      Output:
      get_literature_neighboursResponse (soap:body, use = literal)Source code
      parameters type get_literature_neighboursResponse
      • literature_neighbours_queries type literature_neighbours_queriesType
        • literature_neighbours_per_query - optional, unbounded; type literature_neighbours_per_queryType
          • query_bi_id type int
          • category type string
          • nr_of_neighbours type int
          • literature_neighbours type literature_neighboursType
            • literature_neighbour - optional, unbounded; type literature_neighbourType
              • bi_id type int
              • preferred_name type string
              • alternative_names - optional; type alternative_namesType
                • alternative_name - optional, unbounded; type string
              • entrezgene_id - optional; type int
              • symbol - optional; type string
              • aliases - optional; type aliasesType
                • alias - optional, unbounded; type string
              • organism - optional; type organismType - type string with restriction - enum { 'human', 'mouse', 'rat', 'any' }
                human mouse or rat
              • affymetrix_ids - optional; type affymetrix_idsType
                • affymetrix_id - optional, unbounded; type string
              • ensembl_id - optional; type string
              • literature_count type int
              • r_scaled_score type float
    7. get_literature_network
      Description:
      Generates a graphml-file in which literature neighbours are visualized. The topology of the network is calculated by the GraphViz module using the neato algorithm
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      http://services.nbic.nl/copub/get_literature_network
      Input:
      get_literature_networkRequest (soap:body, use = literal)Source code
      parameters type get_literature_network
      • bi_ids type bi_idsType
        • bi_id - unbounded; type int
        1 or more bi_id of a keyword and/or gene. If genes are used, they must all be of the same organism.
      • categories - optional; type CategoriesType
        • category - unbounded; type string
        The categories to which the neigbours of the bi_ids must belong. Use get_categories operation with purpose is neighbour to get category choices. If bi_ids is a gene then only the gene category of the same organism can be used. Default are disease, pathology, go_bioproc and pathway. If network_type is within then categories are ignored.
      • network_type - optional; type network_typeType - type string with restriction - enum { 'neighbour', 'within', 'intra' }
        Default is neighbour. * neighbour = network of the relations between: 1. query bi_ids, 2. query bi_id and it's neighbours. * within = network of the relations between query bi_ids. * intra = network of the relations between: 1. query bi_ids,2. query bi_id and it's neighbours, 3. neighbour and other neighbour.
      • title - optional; type string
        Default is 'Literature network'
      • literature_count_threshold - optional; type int
        Default 5. Minimal nr of abstracts a cooccurrence must have.
      • r_scaled_score_threshold - optional; type int
        Default 45. Minimal r scaled score a cooccurrence must have.
      • color_seed_nodes - optional; type boolean
        Make node of the bi_ids in the request a distinct color. Default is false.
      • format - optional; type NetworkOutputFormatType - type string with restriction - enum { 'graphml', 'xgmml', 'svg' }
        Default format is xgmml.
      Output:
      get_literature_networkResponse (soap:body, use = literal)Source code
      parameters type get_literature_networkResponse
      • network type base64Binary
    8. get_references
      Description:
      Return medline references where 1 bi_id occures or 2 bi_id occur together References are ordered by pubmed id (mimics ordering by publication date)
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      http://services.nbic.nl/copub/get_references
      Input:
      get_referencesRequest (soap:body, use = literal)Source code
      parameters type get_references
      • bi_id1 type int
      • bi_id2 - optional; type int
      • max_results - optional; type int
        Maximum number of co-occurences to return Default is 25 Max is 100
      • sortdir - optional; type referenceSortType - type string with restriction - enum { 'id:DESC', 'id:ASC', 'bi_count:DESC', 'bi_count:ASC' }
        Order of references. Default is newest first (id:DESC). Can be latest first (id:ASC), most occur. first (bi_count:DESC) or least occur. first (bi_count:ASC).
      Output:
      get_referencesResponse (soap:body, use = literal)Source code
      parameters type get_referencesResponse
      • literature_count type int
      • r_scaled_score - optional; type float
      • references type referencesType
        • reference - optional, unbounded; type referenceType
          • pubmed_id type int
          • title type string
            span tag with class containing bi_id is used to highlight biologicalitem
          • abstract - optional; type string
            span tag with class containing bi_id is used to highlight biologicalitem
          • authors type string
          • date type date
            Create date
          • journal_title type string
          • volume - optional; type string
          • issue - optional; type string
          • page - optional; type string
    9. selftest
      Description:
      Basic functionality of copub is checked. If something is wrong a fault is generated.
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      http://services.nbic.nl/copub/selftest
      Input:
      selftestRequest (soap:body, use = literal)Source code
      parameters type selftest
      Output:
      selftestResponse (soap:body, use = literal)Source code
      parameters type selftestResponse
      • out type boolean
    10. version
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      http://services.nbic.nl/copub/version
      Input:
      versionRequest (soap:body, use = literal)Source code
      parameters type version
      Output:
      versionResponse (soap:body, use = literal)Source code
      parameters type versionResponse
      • literature type string
      • code type string

WSDL source code

<?xml version="1.0"?>
<wsdl:definitions name="copub" targetNamespace="http://services.nbic.nl/copub"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
xmlns:wsdl="http://schemas.xmlsoap.org/wsdl/"
xmlns:tns="http://services.nbic.nl/copub"
xmlns:soap="http://schemas.xmlsoap.org/wsdl/soap/"
>
<wsdl:types>
<xsd:schema targetNamespace="http://services.nbic.nl/copub">
<xsd:element name="get_genes">
<xsd:complexType>
<xsd:sequence>
<xsd:element name="query" type="xsd:string" maxOccurs="1" minOccurs="1">
<xsd:annotation>
<xsd:documentation>Query is exact. Use * as wildcard</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="query_type" type="tns:query_typeType" maxOccurs="1" minOccurs="0">
<xsd:annotation>
<xsd:documentation>Choices symbol, name, entrezgene, ensemblgene, affymetrix. Default name </xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="organism" type="tns:organismType" maxOccurs="1" minOccurs="0">
<xsd:annotation>
<xsd:documentation>Choices are human, mouse, rat or any. Default human</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="max_results" type="xsd:int" maxOccurs="1" minOccurs="0">
<xsd:annotation>
<xsd:documentation> Maximum number of hits per bi_id and category to return Default is 50 Max is 1000 </xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="get_keywords">
<xsd:complexType>
<xsd:sequence>
<xsd:element name="query" type="xsd:string" maxOccurs="1" minOccurs="1">
<xsd:annotation>
<xsd:documentation>Query is exact. Use * as wildcard</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="max_results" type="xsd:int" maxOccurs="1" minOccurs="0">
<xsd:annotation>
<xsd:documentation> Maximum number of keywords to return Default is 50 Max is 1000 </xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="get_categories">
<xsd:complexType>
<xsd:sequence></xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="get_references">
<xsd:complexType>
<xsd:sequence>
<xsd:element name="max_results" type="xsd:int" maxOccurs="1" minOccurs="0">
<xsd:annotation>
<xsd:documentation> Maximum number of co-occurences to return Default is 25 Max is 100 </xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="sortdir" type="tns:referenceSortType" maxOccurs="1" minOccurs="0">
<xsd:annotation>
<xsd:documentation> Order of references. Default is newest first (id:DESC). Can be latest first (id:ASC), most occur. first (bi_count:DESC) or least occur. first (bi_count:ASC). </xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="get_literature_network">
<xsd:complexType>
<xsd:sequence>
<xsd:element name="bi_ids" type="tns:bi_idsType" maxOccurs="1" minOccurs="1">
<xsd:annotation>
<xsd:documentation> 1 or more bi_id of a keyword and/or gene. If genes are used, they must all be of the same organism. </xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="categories" type="tns:CategoriesType" maxOccurs="1" minOccurs="0">
<xsd:annotation>
<xsd:documentation> The categories to which the neigbours of the bi_ids must belong. Use get_categories operation with purpose is neighbour to get category choices. If bi_ids is a gene then only the gene category of the same organism can be used. Default are disease, pathology, go_bioproc and pathway. If network_type is within then categories are ignored. </xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="network_type" type="tns:network_typeType" maxOccurs="1" minOccurs="0">
<xsd:annotation>
<xsd:documentation> Default is neighbour. * neighbour = network of the relations between: 1. query bi_ids, 2. query bi_id and it's neighbours. * within = network of the relations between query bi_ids. * intra = network of the relations between: 1. query bi_ids,2. query bi_id and it's neighbours, 3. neighbour and other neighbour. </xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="title" type="xsd:string" maxOccurs="1" minOccurs="0">
<xsd:annotation>
<xsd:documentation> Default is 'Literature network' </xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="literature_count_threshold" type="xsd:int" maxOccurs="1" minOccurs="0">
<xsd:annotation>
<xsd:documentation> Default 5. Minimal nr of abstracts a cooccurrence must have. </xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="r_scaled_score_threshold" type="xsd:int" maxOccurs="1" minOccurs="0">
<xsd:annotation>
<xsd:documentation> Default 45. Minimal r scaled score a cooccurrence must have. </xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="color_seed_nodes" type="xsd:boolean" maxOccurs="1" minOccurs="0">
<xsd:annotation>
<xsd:documentation> Make node of the bi_ids in the request a distinct color. Default is false. </xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="get_chips">
<xsd:complexType>
<xsd:sequence></xsd:sequence>
</xsd:complexType>
</xsd:element>
</xsd:schema>
</wsdl:types>
<wsdl:portType name="copub">
<wsdl:operation name="get_enriched_keywords">
<wsdl:documentation>Calculates keyword overrepresentation in a set of regulated genes (literature based).</wsdl:documentation>
</wsdl:operation>
<wsdl:operation name="get_genes">
<wsdl:documentation>Search by gene symbol or name or entrezgene/ensembl/affymetri id Return list of genes</wsdl:documentation>
</wsdl:operation>
<wsdl:operation name="get_categories">
<wsdl:documentation>Fetch the list of categories. Note: Not all categories can be used everywhere, use purpose to get the right categories </wsdl:documentation>
</wsdl:operation>
<wsdl:operation name="get_references">
<wsdl:documentation>Return medline references where 1 bi_id occures or 2 bi_id occur together References are ordered by pubmed id (mimics ordering by publication date)</wsdl:documentation>
</wsdl:operation>
<wsdl:operation name="selftest">
<wsdl:documentation>Basic functionality of copub is checked. If something is wrong a fault is generated. </wsdl:documentation>
</wsdl:operation>
<wsdl:operation name="get_literature_network">
<wsdl:documentation>Generates a graphml-file in which literature neighbours are visualized. The topology of the network is calculated by the GraphViz module using the neato algorithm</wsdl:documentation>
</wsdl:operation>
</wsdl:portType>
<wsdl:binding name="copubSOAP" type="tns:copub"></wsdl:binding>
</wsdl:definitions>

About wsdl-viewer.xsl

This document was generated by libxslt XSLT engine. The engine processed the WSDL in XSLT 1.0 compliant mode.
This page has been generated by wsdl-viewer.xsl, version 3.1.01
Author: tomi vanek
Download at http://tomi.vanek.sk/xml/wsdl-viewer.xsl.

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