PubTerm

PubTerm organizes and annotates PubMed abstracts to support curation of biomedical literature focusing on genes, diseases, chemicals, species, and sequence variants.

Key Features:

• Term-based organization: Categorizes abstracts by individual terms, term co-occurrence, or specific phrases for systematic grouping of literature.
• User-defined annotation: Enables annotation and categorization using user-specified categories to record curated information about entities such as genes, diseases, and chemicals.
• Color-coded highlighting: Allows specification of three lists of categories and assignment of colors to highlight different types of information within abstracts.
• Data management and export: Supports saving session information and exporting curated data into various file formats.
• Customizable term view: Organizes abstracts according to biological entities (e.g., genes, diseases, species) to facilitate targeted curation.
• Exploratory views: Provides views that facilitate exploration of abstracts and identification of connections between terms.

Scientific Applications:

• Susceptibility gene curation: Used to curate PubMed abstracts to identify and revise lists of susceptibility genes, for example curating over 400 abstracts mentioning more than 350 genes for pulmonary arterial hypertension.
• Literature review and hypothesis generation: Facilitates comprehensive literature reviews and the detection of term co-occurrence patterns to support hypothesis generation.

Methodology:

Starts from a user-specified PubMed query or list of PubMed identifiers; users define categories and assign colors to highlight information; the system organizes abstracts according to those user-defined categories to enable annotation and categorization.