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Progress in the biomedical sciences is critically dependent on explicit chemical structures and bioactivity results described in text. This applies across drug discovery, pharmacology, chemical......
Progress in the biomedical sciences is critically dependent on explicit chemical structures and bioactivity results described in text. This applies across drug discovery, pharmacology, chemical biology, and metabolomics. However the entombing of the majority of these structures and associated data within patents, papers, abstracts and web pages has been a major barrier to progress. This presentation introduces the current public information flow from documents and its associated barriers, such as inadequate author specification of structures, journal pay walls precluding text mining and the patchiness of MeSH chemistry annotation for PubMed-to-PubChem connectivity. It then reviews trends that are lowering these barriers. These include the Google merge of over 50 million InChIKey(s) from PubChem, ChemSpider and UniChem, ChEMBL containing SAR for 0.8 million structures from 50K medicinal chemistry papers, over 20 million abstracts in PubMed, and full-text open patent chemistry in SureChemOpen bringing PubChem patent-extracted structures to 15 million. In addition, options such as Open Lab Books and figshare are expanding the choices for surfacing new structures. Methods will be outlined for establishing document-to-document and document-to-database links via chemical structures. These include the PubChem toolbox, protein targets in UniProt, PubChem BioAssay, ChEMBL indexing in UK PMC, SureChemOpen, chemicalize.org for text name-to-structure conversion , OSRA for image-to-structure conversion, Venny for set comparisons and InChIKey searching in Google . Combined use of these approaches to make joins between patents, papers, abstracts chemical database entries, SAR data and drug target protein sequences will be illustrated with recent novel antimalarial lead compounds, patent-only BACE2 inhibitors and company code numbers in the NCATS repurposing list.