OmixLitMiner: A Bioinformatics Tool for Prioritizing Biological Leads from ‘Omics Data Using Literature Retrieval and Data Mining

Abstract

Proteomics and genomics discovery experiments generate increasingly large result tables, necessitating more researcher time to convert the biological data into new knowledge. Literature review is an important step in this process and can be tedious for large scale experiments. An informed and strategic decision about which biomolecule targets should be pursued for follow-up experiments thus remains a considerable challenge. To streamline and formalise this process of literature retrieval and analysis of discovery based ‘omics data and as a decision-facilitating support tool for follow-up experiments we present OmixLitMiner, a package written in the computational language R. The tool automates the retrieval of literature from PubMed based on UniProt protein identifiers, gene names and their synonyms, combined with user defined contextual keyword search (i.e., gene ontology based). The search strategy is programmed to allow either strict or more lenient literature retrieval and the outputs are assigned to three categories describing how well characterized a regulated gene or protein is. The category helps to meet a decision, regarding which gene/protein follow-up experiments may be performed for gaining new knowledge and to exclude following already known biomarkers. We demonstrate the tool’s usefulness in this retrospective study assessing three cancer proteomics and one cancer genomics publication. Using the tool, we were able to corroborate most of the decisions in these papers as well as detect additional biomolecule leads that may be valuable for future research.

[Retracted] An Evaluation Model for the Influence Factors of Interest in Literature Courses Based on Data Analysis and Association Rules in a Small‐Sample Environment

“…The core of humanistic spirit is human consciousness, just as the core of modern consciousness is human consciousness. As a modern man, he must have a conscious human consciousness, that is, the humanist spirit of people-oriented [10]. Studying the literature curriculum from the perspective of curriculum theory and putting the selection and determination of literature curriculum into a process of curriculum design will help to observe the selection of literature curriculum from the perspective of literature curriculum objectives.…”

Co-activation of LIN28A and CTNNB1 disturbs cortical neuronal migration and pia mater integrity

“…The associated proteins were further categorised as potential interaction partners with LIN28A (line type): direct protein-protein interaction with LIN28A (Parisi et al, 2021) as mRNA targets of LIN28A (Hafner et al, 2013). Additionally, we used a literature miner pipeline (modified version (Steffen et al, 2020)) to evaluate the background knowledge of these proteins associated with the keyword "cortical development". The proteins were assigned into three categories: 1 = at least one review article; 2 = at least one research article; 3 = no literature found (Steffen et al, 2020).…”

“…5C) (Hafner et al, 2013;Parisi et al, 2021). We further categorised the proteins using a literature mining tool (modified version (Steffen et al, 2020)) to highlight potential proteins of interest (green colour code in Fig. 5C distinguishing between categories: 1 = at least one review paper/well known, 2 = at least one research paper/known, 3 = no further literature available/not known in context of "cortical development" as keyword (Steffen et al, 2020)).…”

Differential regulation of extracellular matrix proteins in three recurrent liver metastases of a single patient with colorectal cancer

“…The tissue distribution of regulated proteins was annotated using the normalized-consensus-transcript-expression-dataset provided by the human protein atlas [ 16 ]. The ECM association of regulated proteins as well as their prognostic value in CRC were investigated by a National Center for Biotechnology Information (NCBI) library-based search using the ‘OmixLitMiner’ tool for literature retrieval [ 17 ] (‘extracellular matrix’ in title or abstract). Afterwards, ECM association was annotated manually.…”