PALM-IST (Pathway Assembly from Literature Mining – an Information Search Tool)

Recently, I found this good research paper called “PALM-IST (Pathway Assembly from Literature Mining – an Information Search Tool) “. Maybe it will be useful for scientists who are interested in this topic.

Sci Rep. 2015 May 19;5:10021. doi: 10.1038/srep10021.

PALM-IST: Pathway Assembly from Literature Mining–an Information Search Tool.


Manual curation of biomedical literature has become extremely tedious process due to its exponential growth in recent years. To extract meaningful information from such large and unstructured text, newer and more efficient mining tool is required. Here, we introduce PALM-IST, a computational platform that not only allows users to explore biomedical abstracts using keyword based text mining but also extracts biological entity (e.g., gene/protein, drug, disease, biological processes, cellular component, etc.) information from the extracted text and subsequently mines various databases to provide their comprehensive inter-relation (e.g., interaction, expression, etc.). PALM-IST constructs protein interaction network and pathway information data relevant to the text search using multiple data mining tools and assembles them to create a meta-interaction network. It also analyzes scientific collaboration by extraction and creation of “co-authorship network,” for a given search context. Hence, this useful combination of literature and data mining provided in PALM-IST can be used to extract novel protein-protein interaction (PPI), to generate meta-pathways and further to identify key crosstalk and bottleneck proteins. PALM-IST is available at

[PubMed – indexed for MEDLINE]

Free PMC Article

PALM-IST (Pathway Assembly from Literature Mining – an Information Search Tool) is a computational platform for users to explore biomedical literature resourse (PubMed) using multiple keywords and extract gene/protein(s) name, drug(s), disease(s) centered information along with their relation/interaction from text and databases. PALM-IST provides users a platform where data and literature mining are performed simultaneously. Combined structured data (from data mining) and unstructured data (from text mining) can be used to extract novel association/interaction between biological entities such as proteins, diseases, or drugs, to generate meta-pathways and further to identify key crosstalk and bottleneck proteins. Further, PALM-IST also enables users to assemble human pathways and protein-protein interaction network (PPIN) using information extracted from text and databases.


1. Real time search in PubMed.
2. Identification and highlighting of genes, drugs and diseases extracted from searched abstracts.
3. Interactive co-occurrence based network of gene-disease, gene-drug, drug-disease from literature.
4. Functional annotation by mapping expression information on to human pathway proteins and their interactors.
5. Platform to merge protein-protein interaction of multiple human genes/proteins.
6. Platform to find cross-talk genes/proteins from merged pathways result.
7. Interactive display of pathways with over-laid with protein-protein interaction information.
8. Interactive display of collaborative network between biomedical experts.