Veupathdb Tools#

Configuration File: veupathdb_tools.json Tool Type: Local Tools Count: 5

This page contains all tools defined in the veupathdb_tools.json configuration file.

Available Tools#

VEuPathDB_get_gene_record (Type: VEuPathDBTool)#

Retrieve the record for a single gene from a VEuPathDB pathogen-genome database by its gene ident…

VEuPathDB_get_gene_record tool specification

Tool Information:

  • Name: VEuPathDB_get_gene_record

  • Type: VEuPathDBTool

  • Description: Retrieve the record for a single gene from a VEuPathDB pathogen-genome database by its gene identifier (primary key), via the EuPathDB WDK gene records endpoint (POST query). Pick the member site with the ‘project’ parameter (plasmodb, toxodb, fungidb, vectorbase, cryptodb, giardiadb, microsporidiadb, piroplasmadb, trichdb, tritrypdb, amoebadb). Returns gene attributes: protein product, organism, gene type, genomic location, chromosome and transcript count. Example: gene_id=’PF3D7_0417200’, project=’plasmodb’ returns the bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) gene of Plasmodium falciparum 3D7.

Parameters:

  • gene_id (string) (required) Gene identifier / primary key (source_id) as used by VEuPathDB. Examples: ‘PF3D7_0417200’ (PlasmoDB), ‘TGME49_200010’ (ToxoDB).

  • project ([‘string’, ‘null’]) (optional) VEuPathDB member site that owns the gene. One of: plasmodb (default), toxodb, fungidb, vectorbase, cryptodb, giardiadb, microsporidiadb, piroplasmadb, trichdb, tritrypdb, amoebadb.

  • attributes ([‘array’, ‘string’, ‘null’]) (optional) Optional list of gene attribute columns to return. Defaults to primary_key, product, organism, gene_type, location_text, source_id. Other valid columns include chromosome, transcript_count, is_pseudo.

Example Usage:

query = {
    "name": "VEuPathDB_get_gene_record",
    "arguments": {
        "gene_id": "example_value"
    }
}
result = tu.run(query)

VEuPathDB_list_gene_searches (Type: BaseRESTTool)#

List all available gene search strategies in VEuPathDB. Returns the search types that can be used…

VEuPathDB_list_gene_searches tool specification

Tool Information:

  • Name: VEuPathDB_list_gene_searches

  • Type: BaseRESTTool

  • Description: List all available gene search strategies in VEuPathDB. Returns the search types that can be used to query genes across pathogen, vector, and host genomes. Each search has a URL segment, display name, description, and the parameters it accepts. Common searches include: GenesByTaxonGene (by organism), GenesFromTranscripts (transform transcript results to genes), and single gene lookups. Use this to discover what types of gene queries are available before constructing searches.

Parameters:

No parameters required.

Example Usage:

query = {
    "name": "VEuPathDB_list_gene_searches",
    "arguments": {
    }
}
result = tu.run(query)

VEuPathDB_list_organism_searches (Type: BaseRESTTool)#

List all available organism search strategies in VEuPathDB. Returns the search types that can be …

VEuPathDB_list_organism_searches tool specification

Tool Information:

  • Name: VEuPathDB_list_organism_searches

  • Type: BaseRESTTool

  • Description: List all available organism search strategies in VEuPathDB. Returns the search types that can be used to query organisms in the VEuPathDB database, covering 785+ pathogen, vector, and host organism genomes. Useful for discovering what organism queries are available. Common searches include: AllOrganisms (list all), GenomeDataTypes (genome statistics), GeneMetrics (gene counts), and OrganismsByText (text search).

Parameters:

No parameters required.

Example Usage:

query = {
    "name": "VEuPathDB_list_organism_searches",
    "arguments": {
    }
}
result = tu.run(query)

VEuPathDB_list_record_types (Type: BaseRESTTool)#

List all available record types in VEuPathDB (Eukaryotic Pathogen, Vector and Host Informatics Re…

VEuPathDB_list_record_types tool specification

Tool Information:

  • Name: VEuPathDB_list_record_types

  • Type: BaseRESTTool

  • Description: List all available record types in VEuPathDB (Eukaryotic Pathogen, Vector and Host Informatics Resources). VEuPathDB is a unified bioinformatics resource for eukaryotic pathogen and host genomics covering Plasmodium (malaria), Toxoplasma, Cryptosporidium, Trypanosoma, Leishmania, fungi, and vector organisms. Returns the available record types (gene, transcript, organism, genomic-sequence, etc.) that can be queried through VEuPathDB’s search API. Encompasses sub-databases: PlasmoDB, ToxoDB, CryptoDB, TriTrypDB, FungiDB, AmoebaDB, MicrosporidiaDB, PiroplasmaDB, GiardiaDB, TrichDB, HostDB, VectorBase, and SchistoDB.

Parameters:

No parameters required.

Example Usage:

query = {
    "name": "VEuPathDB_list_record_types",
    "arguments": {
    }
}
result = tu.run(query)

VEuPathDB_search_genes_by_organism (Type: VEuPathDBTool)#

Search genes belonging to an organism/strain in a VEuPathDB member database using the WDK GenesBy…

VEuPathDB_search_genes_by_organism tool specification

Tool Information:

  • Name: VEuPathDB_search_genes_by_organism

  • Type: VEuPathDBTool

  • Description: Search genes belonging to an organism/strain in a VEuPathDB member database using the WDK GenesByTaxonGene report. Results use offset pagination; metadata reports the true total and, when has_more is true, the next_offset to pass with the same query.

Parameters:

  • organism (string) (required) Full organism/strain name as used by VEuPathDB. Examples: ‘Plasmodium falciparum 3D7’, ‘Toxoplasma gondii ME49’, ‘Aspergillus fumigatus Af293’. Must match the site’s organism vocabulary (genus + species + strain).

  • project ([‘string’, ‘null’]) (optional) VEuPathDB member site to query. One of: plasmodb (default), toxodb, fungidb, vectorbase, cryptodb, giardiadb, microsporidiadb, piroplasmadb, trichdb, tritrypdb, amoebadb.

  • attributes ([‘array’, ‘string’, ‘null’]) (optional) Optional list of gene attribute columns to return. Defaults to primary_key, product, organism, gene_type, location_text, source_id. Other valid columns include chromosome, transcript_count, is_pseudo.

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of genes to return (1-500, default 25).

  • offset (integer) (optional) Zero-based WDK gene result offset. Continue with metadata.next_offset while metadata.has_more is true.

Example Usage:

query = {
    "name": "VEuPathDB_search_genes_by_organism",
    "arguments": {
        "organism": "example_value"
    }
}
result = tu.run(query)