Literature Search for Metabolite
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7.1 years ago


I wish to use a tool/ web-server (if any ?) to extract all metabolites (small molecules)  discussed in scientific literature for their levels/ regulation in a particular cell in plants. Say- parenchyma, mesophylls, meristem, suspension cells etc. This is part of our 'metabolomics effort' where we wish to map everything available in metabolomics as well as traditional biology literature.

Obviously, all such literature do not associate/ discuss/ provide KEGG, HMDB IDs for them, but even common names extraction would help for a cell-to-cell basis in plants. For example, from literature say "Scholar" , or "PubMed" I wish to extract the following information-


Word/ Term      Metabolite     Reference                  Status of cell@      Regulated (if available/ extractable!)
Mesophyll    Proline          Johanna et al. 2002             Stress                    Up
Mesophyll    Glucose           Syamore et al. 2009          Pathogen               Down
Mesophyll    Auxin                Huygens et al. 2009         Ca++ Signalling       Down
Mesophyll    Citric acid       Purita et al. 2015                 Drought                   Up
Mesophyll      Threonine        Andeson et al. 2009          Cell Death                   Down


Many such tools are available in Cytoscape PlugIns like Agilent Literature Search, iHop, WhatzIT, Ploysearch, TEMIS (Commercial), OSCAR, STITCH (comes very close to it!), but then they are all- for genes/ proteins or protein-protein. But nothing on chemical molecules/ metabolites ! I knew, to some extent that PathwayStudios (Araidne Genomics/ now Elsevier) used to do it, but that is commercial and not accessible to me ! I understand a semantic approach, is not it ? I do not wish to map unto pathways, but extract only the names, IDs to the cell-sepcificity and regulations in the form of a network or a .csv/text file !


Any advice on how to approach this problem ! I would highly appreciate any quick insights/ thoughts.

Thanks a lot in advance, ; )


semantics literature query KEGG pubmed • 1.4k views

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