Epmc Annotations Tools#

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

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

Available Tools#

EPMC_get_article_chemicals (Type: EPMCAnnotationsTool)#

Get chemicals and drugs mentioned in a biomedical article, identified by text mining from Europe …

EPMC_get_article_chemicals tool specification

Tool Information:

  • Name: EPMC_get_article_chemicals

  • Type: EPMCAnnotationsTool

  • Description: Get chemicals and drugs mentioned in a biomedical article, identified by text mining from Europe PMC. Returns chemical/drug names with database links and mention frequency. Example: pmid=’33332779’ returns tocilizumab, dexamethasone, etc.

Parameters:

  • pmid (string) (optional) PubMed ID (e.g., ‘33332779’).

  • pmcid (string) (optional) PubMed Central ID (e.g., ‘PMC7781101’). Alternative to pmid.

Example Usage:

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

EPMC_get_article_diseases (Type: EPMCAnnotationsTool)#

Get the complete deduplicated set of diseases mentioned in a biomedical article, identified by Eu…

EPMC_get_article_diseases tool specification

Tool Information:

  • Name: EPMC_get_article_diseases

  • Type: EPMCAnnotationsTool

  • Description: Get the complete deduplicated set of diseases mentioned in a biomedical article, identified by Europe PMC text mining. Returns disease names, ontology links, mention frequency, and accurate total/returned counts without a hidden top-30 cap.

Parameters:

  • pmid (string) (optional) PubMed ID (e.g., ‘33332779’).

  • pmcid (string) (optional) PubMed Central ID (e.g., ‘PMC7781101’). Alternative to pmid.

Example Usage:

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

EPMC_get_article_genes (Type: EPMCAnnotationsTool)#

Get the complete deduplicated set of genes and proteins mentioned in a biomedical article, identi…

EPMC_get_article_genes tool specification

Tool Information:

  • Name: EPMC_get_article_genes

  • Type: EPMCAnnotationsTool

  • Description: Get the complete deduplicated set of genes and proteins mentioned in a biomedical article, identified by Europe PMC text mining. Returns names, links, mention frequency, total_entities, and returned_entities without a hidden top-30 cap.

Parameters:

  • pmid (string) (optional) PubMed ID (e.g., ‘33332779’).

  • pmcid (string) (optional) PubMed Central ID (e.g., ‘PMC7781101’). Alternative to pmid.

Example Usage:

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

EPMC_get_article_organisms (Type: EPMCAnnotationsTool)#

Get organisms mentioned in a biomedical article, identified by text mining from Europe PMC. Retur…

EPMC_get_article_organisms tool specification

Tool Information:

  • Name: EPMC_get_article_organisms

  • Type: EPMCAnnotationsTool

  • Description: Get organisms mentioned in a biomedical article, identified by text mining from Europe PMC. Returns organism names with NCBI Taxonomy links and mention frequency. Example: pmid=’33332779’ returns SARS-CoV-2, Homo sapiens, etc.

Parameters:

  • pmid (string) (optional) PubMed ID (e.g., ‘33332779’).

  • pmcid (string) (optional) PubMed Central ID (e.g., ‘PMC7781101’). Alternative to pmid.

Example Usage:

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

EPMC_get_text_mined_annotations (Type: EPMCAnnotationsTool)#

Get all unique text-mined annotations from a biomedical article via Europe PMC. Returns the compl…

EPMC_get_text_mined_annotations tool specification

Tool Information:

  • Name: EPMC_get_text_mined_annotations

  • Type: EPMCAnnotationsTool

  • Description: Get all unique text-mined annotations from a biomedical article via Europe PMC. Returns the complete deduplicated gene/protein, disease, chemical, organism, GO, and EFO entity sets with mention counts; annotation_counts reports each full group size. Example: PMC5500808 returns more than 70 unique gene/protein entities without silent capping.

Parameters:

  • pmid (string) (optional) PubMed ID (e.g., ‘33332779’). Either pmid or pmcid is required.

  • pmcid (string) (optional) PubMed Central ID (e.g., ‘PMC7781101’). Alternative to pmid.

  • annotation_type (string) (optional) Filter by annotation type. Options: ‘Gene_Proteins’, ‘Diseases’, ‘Chemicals’, ‘Organisms’, ‘Gene_Ontology’, ‘EFO’. Leave empty for all types.

Example Usage:

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