Web Service: copub

Port type copubSource code

1. get_categories
   Source code
   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
   Source code
   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
   Source code
   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
   Source code
   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
   Source code
   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
   Source code
   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
   Source code
   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
   Source code
   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
   Source code
   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
    Source code
    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