<b>Python workflows (Jupyter notebooks) for multi-database phytochemical integration and curation: Dr. Duke processing, IMPPAT extraction, and PubChem enrichment</b>

This Figshare deposit provides the complete Jupyter Notebook–based computational workflows used to generate the phytochemical profiling datasets sourced from a certain venereal disease ethnobotanical study in Okitipupa LGa, Nigeria. The notebooks implement reproducible Python pipelines for (i) filtering and integrating Dr. Duke database components and (ii) extracting, enriching, and standardising phytochemical records from IMPPAT and other databases using PubChem.

For clarity and reuse, the notebooks are organised into two internal sections, corresponding to their functional roles within the multi-database workflow.

Contents (structured as two [progressive internal sections from certain raw dataset published elsewhere):

Section D: Dr. Duke integration notebooks

This section contains staged Python notebooks implementing the Dr. Duke data-integration pipeline. The notebooks progressively generate the intermediate and final Dr. Duke-derived outputs from raw phytochemical datasets published elsewhere.

Included notebooks:

• Script1A (FNFTAX1): filtering raw taxon tables to study species
• Script1B (FNFTAX2): joining taxa with ethnobotanical uses and phytochemicals
• Script1C (FNFTAX3): decoding plant-part codes and appending dosage/toxicity fields
• Script1D (FNFTAX4): aggregating biological activity fields and expanding references

Together, these notebooks provide a transparent and auditable computational record of Dr. Duke dataset curation.

Section E: IMPPAT extraction and PubChem enrichment notebooks

This section contains notebooks supporting the IMPPAT arm of the multi-database workflow and molecular metadata enrichment

Included notebooks:

• Script 2: IMPPAT extraction notebook: automated extraction and formatting of IMPPAT phytochemical records relevant to study taxa
• Script 3: PubChem enrichment notebook: programmatic retrieval and integration of molecular properties (molecular weight, molecular formula, IUPAC name) to standardise compound identifiers

These notebooks enable compound-level standardisation and filtering of phytochemicals suitable for downstream docking and cheminformatic analyses.