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PubMed abstract sifter: an API-driven literature mining tool for biomedical and biochemical research
Citation:
Baker, N. PubMed abstract sifter: an API-driven literature mining tool for biomedical and biochemical research. Fall ACS, Chicago, IL, August 21 - 25, 2022. https://doi.org/10.23645/epacomptox.20481642
Impact/Purpose:
PubMed Abstract Sifter: an API-driven literature mining tool for biomedical and biochemical research This is a CINF Collaborative symposium for a Convergent Research Community for joint inter-divisional programming in conjunction with CATL, COMP and PHYS on the general topic of Open Software. This CINF symposium will discuss open sources for data sets, data accessibly, websites, APIs, Open software for chemistry information and data analysis available through shared repositories, freely shared data, information and collaborate open data sharing projects.
Description:
While data about chemicals is increasingly being housed in structured databases, the rich information about the effects of chemicals on biological systems largely remains in the unstructured text of the biomedical and biochemical literature. The EPA’s Center for Computational Toxicology has developed the PubMed Abstract Sifter, a publicly available literature mining tool that facilitates the task of searching the millions of publication records, triaging the results, and extracting relevant information from them. The tool uses NCBI APIs to query and retrieve from PubMed. Clowder based APIs are used to facilitate the extraction of substance MeSH terms from the returned corpus of articles, and finally EPA’s API calls can take a list of chemicals and search for them on the DSSTox database and return data on properties, structure, and in vitro testing. The toxicity literature for the resulting set of chemicals can be retrieved and chemicals ranked on the results. The Abstract Sifter and the EPA’s Chemicals Dashboard are available at comptox.epa.gov/dashboard. This abstract does not necessarily represent US EPA policy.
URLs/Downloads:
DOI: PubMed abstract sifter: an API-driven literature mining tool for biomedical and biochemical research
ACS_BAKER_CINF_FINAL.PDF (PDF, NA pp, 2209.929 KB, about PDF)