Overview of the gene ontology task at BioCreative IV

Gene Ontology (GO) annotation is a common task among model organism databases (MODs) for capturing gene function data from journal articles. It is a time-consuming and labor-intensive task, and is thus often considered as one of the bottlenecks in literature curation. There is a growing need for semiautomated or fully automated GO curation techniques that will help database curators to rapidly and accurately identify gene function information in full-length articles. Despite multiple attempts in the past, few studies have proven to be useful with regard to assisting real-world GO curation. The shortage of sentence-level training data and opportunities for interaction between text-mining developers and GO curators has limited the advances in algorithm development and corresponding use in practical circumstances. To this end, we organized a text-mining challenge task for literature-based GO annotation in BioCreative IV. More specifically, we developed two subtasks: (i) to automatically locate text passages that contain GO-relevant information (a text retrieval task) and (ii) to automatically identify relevant GO terms for the genes in a given article (a concept-recognition task). With the support from five MODs, we provided teams with >4000 unique text passages that served as the basis for each GO annotation in our task data. Such evidence text information has long been recognized as critical for text-mining algorithm development but was never made available because of the high cost of curation. In total, seven teams participated in the challenge task. From the team results, we conclude that the state of the art in automatically mining GO terms from literature has improved over the past decade while much progress is still needed for computer-assisted GO curation. Future work should focus on addressing remaining technical challenges for improved performance of automatic GO concept recognition and incorporating practical benefits of text-mining tools into real-world GO annotation

Identifying Relevant Evidence for Systematic Reviews and Review Updates

Systematic reviews identify, assess and synthesise the evidence available to answer complex research questions. They are essential in healthcare, where the volume of evidence in scientific research publications is vast and cannot feasibly be identified or analysed by individual clinicians or decision makers. However, the process of creating a systematic review is time consuming and expensive. The pace of scientific publication in medicine and related fields also means that evidence bases are continually changing and review conclusions can quickly become out of date. Therefore, developing methods to support the creating and updating of reviews is essential to reduce the workload required and thereby ensure that reviews remain up to date. This research aims to support systematic reviews, thus improving healthcare through natural language processing and information retrieval techniques. More specifically, this thesis aims to support the process of identifying relevant evidence for systematic reviews and review updates to reduce the workload required from researchers. This research proposes methods to improve studies ranking for systematic reviews. In addition, this thesis describes a dataset of systematic review updates in the field of medicine created using 25 Cochrane reviews. Moreover, this thesis develops an algorithm to automatically refine the Boolean query to improve the identification of relevant studies for review updates. The research demonstrates that automating the process of identifying relevant evidence can reduce the workload of conducting and updating systematic reviews