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, ; )