Global S&T Development Trend Analysis Platform of Resources and Environment
DOI | 10.1289/EHP4713 |
Generating the Blood Exposome Database Usinga Comprehensive Text Mining and Database Fusion Approach | |
Barupal, Dinesh Kumar; Fiehn, Oliver | |
2019-09-01 | |
发表期刊 | ENVIRONMENTAL HEALTH PERSPECTIVES |
ISSN | 0091-6765 |
EISSN | 1552-9924 |
出版年 | 2019 |
卷号 | 127期号:9 |
文章类型 | Article |
语种 | 英语 |
国家 | USA |
英文摘要 | BACKGROUND: Blood chemicals are routinely measured in clinical or preclinical research studies to diagnose diseases, assess risks in epidemiological research, or use metabolomic phenotyping in response to treatments. A vast volume of blood-related literature is available via the PubMed database for data mining. OBJECTIVES: We aimed to generate a comprehensive blood exposome database of endogenous and exogenous chemicals associated with the mammalian circulating system through text mining and database fusion. METHODS: Using NCBI resources, we retrieved PubMed abstracts, PubChem chemical synonyms, and PMC supplementary tables. We then employed text mining and PubChem crowdsourcing to associate phrases relating to blood with PubChem chemicals. False positives were removed by a phrase pattern and a compound exclusion list. RESULTS: A query to identify blood-related publications in the PubMed database yielded 1.1 million papers. Matching a total of 15 million synonyms from 6.5 million relevant PubChem chemicals against all blood-related publications yielded 37,514 chemicals and 851,999 publications records. Mapping PubChem compound identifiers to the PubMed database yielded 49,940 unique chemicals linked to 676,643 papers. Analysis of open-access metabolomics papers related to blood phrases in the PMC database yielded 4,039 unique compounds and 204 papers. Consolidating these three approaches summed up to a total of 41,474 achiral structures that were linked to 65,957 PubChem CIDs and to over 878,966 PubMed articles. We mapped these compounds to 50 databases such as those covering metabolites and pathways, governmental and toxicological databases, pharmacology resources, and bioassay repositories. In comparison, HMDB, the Human Metabolome Database, links 1,075 compounds to blood-related primary publications. CONCLUSION: This new Blood Exposome Database can be used for prioritizing chemicals for systematic reviews, developing target assays in exposome research, identifying compounds in untargeted mass spectrometry, and biological interpretation in metabolomics data. |
领域 | 资源环境 |
收录类别 | SCI-E |
WOS记录号 | WOS:000488971900005 |
WOS关键词 | MASS-SPECTROMETRY ; AMINO-ACIDS ; METABOLITES ; RISK ; IDENTIFICATION ; ASSOCIATIONS ; INFORMATICS ; GENOME ; TRENDS ; CANCER |
WOS类目 | Environmental Sciences ; Public, Environmental & Occupational Health ; Toxicology |
WOS研究方向 | Environmental Sciences & Ecology ; Public, Environmental & Occupational Health ; Toxicology |
引用统计 | |
文献类型 | 期刊论文 |
条目标识符 | http://119.78.100.173/C666/handle/2XK7JSWQ/186591 |
专题 | 资源环境科学 |
作者单位 | Univ Calif Davis, NIH, West Coast Metabol Ctr, Genome Ctr, Davis, CA 95616 USA |
推荐引用方式 GB/T 7714 | Barupal, Dinesh Kumar,Fiehn, Oliver. Generating the Blood Exposome Database Usinga Comprehensive Text Mining and Database Fusion Approach[J]. ENVIRONMENTAL HEALTH PERSPECTIVES,2019,127(9). |
APA | Barupal, Dinesh Kumar,&Fiehn, Oliver.(2019).Generating the Blood Exposome Database Usinga Comprehensive Text Mining and Database Fusion Approach.ENVIRONMENTAL HEALTH PERSPECTIVES,127(9). |
MLA | Barupal, Dinesh Kumar,et al."Generating the Blood Exposome Database Usinga Comprehensive Text Mining and Database Fusion Approach".ENVIRONMENTAL HEALTH PERSPECTIVES 127.9(2019). |
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