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Background: Whatizit is a text processing system that allows you to do text-mining tasks on text. It is great at identifying molecular biology terms and linking them to publicly available databases. Identified terms are wrapped with XML tags that carry additional information, such as the primary keys to the databases where all the relevant information is kept. The wrapping XML is translated into HTML hypertext links. This service is highly appreciated by people who are reading literature and need to quickly find more information about a particular term, e.g. its Gene Ontology term. Whatizit is used in identifying formalized language patterns, specialized, syntactically formalized, technical notation. The annotation speed of a given pipeline is almost independent of the size of the vocabulary behind it and is currently based on pattern matching. In addition, several vocabularies can be integrated in a single pipeline. Methodology: The pipeline used is comprised of 175k Gene Ontology terms (preferred labels + synonyms). The annotation on Medline 2015-2019 corpus is done with Gene Ontology (GO) integrated dictionary. The .zip file contains 10 XML files - each file is for half an year of MEDLINE annotated abstracts. In addition to the abstract, the title is also annotated for further information enrichment. Respective DOIs, PMIDs are also included in the XML, when applicable. Further development: The XML files can be converted into JSON, JSON-LD format.
Gene Ontology, annotation, named-entity recognition, Medline, text mining, tagging
Gene Ontology, annotation, named-entity recognition, Medline, text mining, tagging
| selected citations These citations are derived from selected sources. This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically). | 0 | |
| popularity This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network. | Average | |
| influence This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically). | Average | |
| impulse This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network. | Average |
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