{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,3]],"date-time":"2025-06-03T10:23:55Z","timestamp":1748946235483},"reference-count":35,"publisher":"World Scientific Pub Co Pte Lt","issue":"05","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2017,10]]},"abstract":"<jats:p> Due to the importance of post-translational modifications (PTMs) in human health and diseases, PTMs are regularly reported in the biomedical literature. However, the continuing and rapid pace of expansion of this literature brings a huge challenge for researchers and database curators. Therefore, there is a pressing need to aid them in identifying relevant PTM information more efficiently by using a text mining system. So far, only a few web servers are available for mining information of a very limited number of PTMs, which are based on simple pattern matching or pre-defined rules. In our work, in order to help researchers and database curators easily find and retrieve PTM information from available text, we have developed a text mining tool called MPTM, which extracts and organizes valuable knowledge about 11 common PTMs from abstracts in PubMed by using relations extracted from dependency parse trees and a heuristic algorithm. It is the first web server that provides literature mining service for hydroxylation, myristoylation and GPI-anchor. The tool is also used to find new publications on PTMs from PubMed and uncovers potential PTM information by large-scale text analysis. MPTM analyzes text sentences to identify protein names including substrates and protein-interacting enzymes, and automatically associates them with the UniProtKB protein entry. To facilitate further investigation, it also retrieves PTM-related information, such as human diseases, Gene Ontology terms and organisms from the input text and related databases. In addition, an online database (MPTMDB) with extracted PTM information and a local MPTM Lite package are provided on the MPTM website. MPTM is freely available online at http:\/\/bioinformatics.ustc.edu.cn\/mptm\/ and the source codes are hosted on GitHub: https:\/\/github.com\/USTC-HILAB\/MPTM . <\/jats:p>","DOI":"10.1142\/s0219720017400054","type":"journal-article","created":{"date-parts":[[2017,9,12]],"date-time":"2017-09-12T03:32:55Z","timestamp":1505187175000},"page":"1740005","source":"Crossref","is-referenced-by-count":8,"title":["MPTM: A tool for mining protein post-translational modifications from literature"],"prefix":"10.1142","volume":"15","author":[{"given":"Dongdong","family":"Sun","sequence":"first","affiliation":[{"name":"School of Information Science and Technology, University of Science and Technology of China, Hefei, Anhui 230027, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Minghui","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Information Science and Technology, University of Science and Technology of China, Hefei, Anhui 230027, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ao","family":"Li","sequence":"additional","affiliation":[{"name":"School of Information Science and Technology, University of Science and Technology of China, Hefei, Anhui 230027, P. R. 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