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Fig. 1 | Microbiome

Fig. 1

From: A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space

Fig. 1

Public domain mining workflow for identifying intestinal bacteria, known or suggested to exert beneficial effects on the infant immune system. The main scientific concepts for the project were categorized into four research topics: (a) infant gut microbiome, (b) infant nutrition and microbiome metabolism, (c) beneficial bacteria supporting immune system development in infants, and (d) beneficial bacteria preventing infections in infants. For each topic, a set of keywords was identified to retrieve all relevant publications from MEDLINE, PubMed, and PubMed Central. All relevant terms, belonging to the entities: diseases, genes, chemicals, and species, were annotated. Specific dictionaries were then created selecting all terms relevant for the present study. Sentences showing a relationship between dictionary concepts were extracted from the texts through natural language processing. The output is a list of sentences with the following related pieces of information: PubMed ID, journal section, terms in the relationships and, for each dictionary, the list of terms found

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