Textpresso for Neuroscience: Searching the Full Text of Thousands of Neuroscience Research Papers

Textpresso is a text-mining system for scientific literature. Its two major features are access to the full text of research papers and the development and use of categories of biological concepts as well as categories that describe or relate objects. A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature. Here we describe Textpresso for Neuroscience, part of the core Neuroscience Information Framework (NIF). The Textpresso site currently consists of 67,500 full text papers and 131,300 abstracts. We show that using categories in literature can make a pure keyword query more refined and meaningful. We also show how semantic queries can be formulated with categories only. We explain the build and content of the database and describe the main features of the web pages and the advanced search options. We also give detailed illustrations of the web service developed to provide programmatic access to Textpresso. This web service is used by the NIF interface to access Textpresso. The standalone website of Textpresso for Neuroscience can be accessed at http://www.textpresso.org/neuroscience

Evidence/Discovery-Based Evolving Ontology (EDBEO)

This paper presents a proposal for the development of an ontology evolution strategy which refines ontological relations in scientific ontologies. In addition to experts’ consensus, it is desirable to define ontological relations between any two concepts in a scientific ontology based on scientific evidence. To address this issue, we can relate ontological relations to different research results obtained from various studies. To implement this solution, our envisaged evidence/discovery-based methodology integrates a higher-level ontology (systematic review ontology) into a systematic review agent which employs a Fuzzy Inference System in order to automatically modifyontological relations of a domain ontology based on the evidence received from information resources. The evidence/discovery-based methodology will further use the domain ontology to discover novel connections between distinct literatures, thereby, enrich its conceptualization

Knowledge-based Biomedical Data Science 2019

Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity.Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages with 3 table

PPLook: an automated data mining tool for protein-protein interaction

<p>Abstract</p> <p>Background</p> <p>Extracting and visualizing of protein-protein interaction (PPI) from text literatures are a meaningful topic in protein science. It assists the identification of interactions among proteins. There is a lack of tools to extract PPI, visualize and classify the results.</p> <p>Results</p> <p>We developed a PPI search system, termed PPLook, which automatically extracts and visualizes protein-protein interaction (PPI) from text. Given a query protein name, PPLook can search a dataset for other proteins interacting with it by using a keywords dictionary pattern-matching algorithm, and display the topological parameters, such as the number of nodes, edges, and connected components. The visualization component of PPLook enables us to view the interaction relationship among the proteins in a three-dimensional space based on the OpenGL graphics interface technology. PPLook can also provide the functions of selecting protein semantic class, counting the number of semantic class proteins which interact with query protein, counting the literature number of articles appearing the interaction relationship about the query protein. Moreover, PPLook provides heterogeneous search and a user-friendly graphical interface.</p> <p>Conclusions</p> <p>PPLook is an effective tool for biologists and biosystem developers who need to access PPI information from the literature. PPLook is freely available for non-commercial users at <url>http://meta.usc.edu/softs/PPLook</url>.</p

Application of Biomedical Text Mining

With the enormous volume of biological literature, increasing growth phenomenon due to the high rate of new publications is one of the most common motivations for the biomedical text mining. Aiming at this massive literature to process, it could extract more biological information for mining biomedical knowledge. Using the information will help understand the mechanism of disease generation, promote the development of disease diagnosis technology, and promote the development of new drugs in the field of biomedical research. Based on the background, this chapter introduces the rise of biomedical text mining. Then, it describes the biomedical text-mining technology, namely natural language processing, including the several components. This chapter emphasizes the two aspects in biomedical text mining involving static biomedical information recognization and dynamic biomedical information extraction using instance analysis from our previous works. The aim is to provide a way to quickly understand biomedical text mining for some researchers

Integration of breast cancer gene signatures based on graph centrality

<p>Abstract</p> <p>Background</p> <p>Various gene-expression signatures for breast cancer are available for the prediction of clinical outcome. However due to small overlap between different signatures, it is challenging to integrate existing disjoint signatures to provide a unified insight on the association between gene expression and clinical outcome.</p> <p>Results</p> <p>In this paper, we propose a method to integrate different breast cancer gene signatures by using graph centrality in a context-constrained protein interaction network (PIN). The context-constrained PIN for breast cancer is built by integrating complete PIN and various gene signatures reported in literatures. Then, we use graph centralities to quantify the importance of genes to breast cancer. Finally, we get reliable gene signatures that are consisted by the genes with high graph centrality. The genes which are well-known breast cancer genes, such as TP53 and BRCA1, are ranked extremely high in our results. Compared with previous results by functional enrichment analysis, graph centralities, especially the eigenvector centrality and subgraph centrality, based gene signatures are more tightly related to breast cancer. We validate these signatures on genome-wide microarray dataset and found strong association between the expression of these signature genes and pathologic parameters.</p> <p>Conclusions</p> <p>In summary, graph centralities provide a novel way to connect different cancer signatures and to understand the mechanism of relationship between gene expression and clinical outcome of breast cancer. Moreover, this method is not only can be used on breast cancer, but also can be used on other gene expression related diseases and drug studies.</p

Network based integrated analysis of phenotype-genotype data for prioritization of candidate symptom genes

YesSymptoms and signs (symptoms in brief) are the essential clinical manifestations for individualized diagnosis and treatment in traditional Chinese medicine (TCM). To gain insights into the molecular mechanism of symptoms, we develop a computational approach to identify the candidate genes of symptoms. This paper presents a network-based approach for the integrated analysis of multiple phenotype-genotype data sources and the prediction of the prioritizing genes for the associated symptoms. The method first calculates the similarities between symptoms and diseases based on the symptom-disease relationships retrieved from the PubMed bibliographic database. Then the disease-gene associations and protein-protein interactions are utilized to construct a phenotype-genotype network. The PRINCE algorithm is finally used to rank the potential genes for the associated symptoms. The proposed method gets reliable gene rank list with AUC (area under curve) 0.616 in classification. Some novel genes like CALCA, ESR1, and MTHFR were predicted to be associated with headache symptoms, which are not recorded in the benchmark data set, but have been reported in recent published literatures. Our study demonstrated that by integrating phenotype-genotype relationships into a complex network framework it provides an effective approach to identify candidate genes of symptoms.NSFC Project (61105055, 81230086), China 973 Program (2014CB542903), The National Key Technology R&D Program (2013BAI02B01, 2013BAI13B04), the National S&T Major Special Project on Major New Drug Innovation (2012ZX09503-001-003), and the Fundamental Research Funds for the Central Universities

Mining Disease Associated Biomarker Networks from PubMed

Abstract-Disease related biomarker discovery is the critical step to realize the future personalized medicine and has been an important research area. With exponential growing of biomedical knowledge deposited in PubMed database, it is now an essential step to mine PubMed for biomarker-disease associations to support the laboratory research and clinical validation. We constructed list of human diseases that are most frequently associated with biomarker in literatures by text mining. Top ranked neurology diseases were then used to extract associated genes from PubMed using context sensitive information retrieval methods. Associated genes were then integrated into pathways and subject to network biomarker analysis. Our approach identifies both known and potential biomarkers for 3 neurodegenerative diseases