TPX: Biomedical literature search made easy

TPX is a web-based PubMed search enhancement tool that enables faster article searching using analysis and exploration features. These features include identification of relevant biomedical concepts from search results with linkouts to source databases, concept based article categorization, concept assisted search and filtering, query refinement. A distinguishing feature here is the ability to add user-defined concept names and/or concept types for named entity recognition. The tool allows contextual exploration of knowledge sources by providing concept association maps derived from the MEDLINE repository. It also has a full-text search mode that can be configured on request to access local text repositories, incorporating entity co-occurrence search at sentence/paragraph levels. Local text files can also be analyzed on-the-fly. Availability: http://tpx.atc.tcs.com     

从文献计量学角度评价我国干细胞产业发展历程

目的:通过分析我国有关干细胞科技论文被国际权威检索工具PubMed收录情况,评价我国干细胞领域的发展历程及应用前景。方法:应用文献计量学和数理统计方法对PubMed收录我国干细胞领域科技论文进行统计分析。结果:PubMed一共收录我国干细胞领域科技论文8039篇,其中中文文献2021篇,外文文献6018篇;北京、上海、广东、台湾四个地区发文量领先于其他地区;排名前三的发文机构为中山大学、上海交通大学和中国医学科学院北京协和医院;国际期刊分布中Biochem Biophys Res Commun、Biomaterials、PLoS One位列前三甲;国内期刊分布中中国实验血液学杂志、中国修复重建外科杂志、中华医学杂志位列前三甲;主题分布中高频主题词有间充质干细胞、骨髓细胞、造血干细胞,等;干细胞治疗疾病常见的有白血病、心肌梗死、肝肿瘤,等。结论:我国干细胞起步于1986年,于2000年后快速发展,发文量成几何倍数增长,干细胞的发展将对我国传统医疗手段和医疗观念造成一场重大的革命。     

基于CNKI和PubMed数据库的双歧杆菌研究文献分析

目的统计分析国内外已发表的与双歧杆菌相关的期刊文献,了解其中的研究热点与发展趋势,为相关科研工作者提供参考。方法研究资料来源于CNKI和PubMed数据库,应用文献计量学的方法对两个数据库所收录的双歧杆菌相关文献进行分析。结果截至2018年8月15日,CNKI和PubMed分别收录了9277和5130篇相关文献。在数量上,国内外对双歧杆菌的研究都从20世纪90年代开始快速增长。从学科分布和关键词来看,中外研究共同关注了消化道疾病和儿科学,同时中外研究侧重点又有明显的差异。国内研究机构参与发表在国际杂志上的文章数量较多,但是其中作为第一发表单位的文章数量偏少。结论双歧杆菌相关的基础与应用研究还有许多需要深入和拓展的方面,研究者应当在相关领域进行实质性突破。     

一种基于MeSH主题词的临床?鄄组学关系挖掘方法

癌症的发生发展与机体内基因的改变有密切联系,在临床上表现为症状或检测指标的异常．通过挖掘分析临床表现与基因改变之间的关系,可为癌症早期诊断和精准治疗提供临床决策支持．从文献数据出发,利用结论性数据挖掘基因与临床表现的关系具有重要意义．本文提出一种基于医学主题词(Medical Subject Headings,MeSH)的生物医学实体关系挖掘方法．该方法利用PubMed中提供的文献信息,借用向量空间模型思想,使用MeSH主题词矢量表达待研究实体,引入文献相互引用因素对结果进行修正,将关系挖掘转化为矢量间的数学运算,实现定量分析．本文将该方法应用于结直肠癌临床表现和基因关系的研究中,得到与结直肠癌相关的203个基因和对应的临床-基因462个关系．通过结合使用基因功能和通路分析工具g:Profiler和KEGG等,对结果进行分析验证．结果表明,基于MeSH主题词的文献挖掘方法,避免传统“共现”方法对发现潜在关系的限制和复杂语义分析带来的大量计算,为生物实体之间潜在关系的挖掘提供一种新的思路和方法．     

Clustering of PubMed abstracts using nearer terms of the domain

Literature search is a process in which external developers provide alternative representations for efficient data mining of biomedical literature such as ranking search results, displaying summarized knowledge of semantics and clustering results into topics. In clustering search results, prominent vocabularies, such as GO (Gene Ontology), MeSH(Medical Subject Headings) and frequent terms extracted from retrieved PubMed abstracts have been used as topics for grouping. In this study, we have proposed FNeTD (Frequent Nearer Terms of the Domain) method for PubMed abstracts clustering. This is achieved through a two-step process viz; i) identifying frequent words or phrases in the abstracts through the frequent multi-word extraction algorithm and ii) identifying nearer terms of the domain from the extracted frequent phrases using the nearest neighbors search. The efficiency of the clustering of PubMed abstracts using nearer terms of the domain was measured using F-score. The present study suggests that nearer terms of the domain can be used for clustering the search results.     

Contextualizing the Genes Altered in Bladder Neoplasms in Pediatric andTeen Patients Allows Identifying Two Main Classes of Biological ProcessesInvolved and New Potential Therapeutic Targets

Research on bladder neoplasms in pediatric and teen patients (BNPTP) has described 21 genes, which are variously involved in this disease and are mostly responsible for deregulated cell proliferation. However, due to the limited number of publications on this subject, it is still unclear what type of relationships there are among these genes and which are the chances that, while having different molecular functions, they i) act as downstream effector genes of well-known pro- or anti- proliferative stimuli and/or interplay with biochemical pathways having oncological relevance or ii) are specific and, possibly, early biomarkers of these pathologies. A Gene Ontology (GO)-based analysis showed that these 21 genes are involved in biological processes, which can be split into two main classes: cell regulation-based and differentiation/development-based. In order to understand the involvement/overlapping with main cancer-related pathways, we performed a meta-analysis dependent on the 189 oncogenic signatures of the Molecular Signatures Database (OSMSD) curated by the Broad Institute. We generated a binary matrix with 53 gene signatures having at least one hit; this analysis i) suggests that some genes of the original list show inconsistencies and might need to be experimentally re- assessed or evaluated as biomarkers (in particular, ACTA2) and ii) allows hypothesizing that important (proto)oncogenes (E2F3, ERBB2/HER2, CCND1, WNT1, and YAP1) and (putative) tumor suppressors (BRCA1, RBBP8/CTIP, and RB1-RBL2/p130) may participate in the onset of this disease or worsen the observed phenotype, thus expanding the list of possible molecular targets for the treatment of BNPTP.     

基于社会网络分析和共词分析的制药技术领域研究

目的:深入研究制药技术领域的发展态势。方法:本研究以Pub Med数据库中收录的制药技术领域研究论文为研究对象,采用社会网络分析、共词分析等定量方法,结合药学专业知识的定性分析,从论文数量年度分布、国家/地区分布及合作网络、研究主题等多个角度开展研究。结果:研究发现:第一,全球制药技术领域共有研究论文95381篇,近几年正处于快速发展阶段;第二,论文发表集中在美国、中国和日本等国家;第三,在定量分析的基础上,结合药学专业知识,共得到15个研究主题,包括点击化学、晶型药物、纳米微球药物等。结论:美国在制药技术领域处于主导地位,中国发文量已经具备一定优势,但发文量和国际影响力与美国相比还是存在较大差距;通过对制药技术领域研究主题的深入分析可以全面把握制药技术领域的研究现状和发展态势。